Sidd and CJ turning to face you when they don't acknowledge you in their conversation feels a bit odd.
I think bit of rearranging the Jump to commands when first talking to Alex would be nice. (for example, after selecting help- run, it'd be better to jump back to the help options rather than back to "anything you'd like to ask about?")
The "Would you like to save?" prompt with the jam jars is unnecessary, because the "Call Save Screen" command also asks if you want to save, so I have to respond "Yes" twice to save once. (Not a big deal, of course, especially now that I know about the length of the game, but when I was starting off I was saving like, every time I passed a jar because I was worried save points would be rare lmfao)
Speaking of saving, it does still display the map's name, and it feels a bit awkward to see map names like "TownNightAct1" instead of just "Brownsville". Of course, their current names are way better for organization, and there's not many named locations, so it'd probably be easier to just modify the save screen to not display the map instead. (Similarly, the load screen shows the player's dex and badge count)
This is incredibly minor, but I don't think "insinuate" is really a word that would come up in casual conversation lol, might just be me, though.
Ben's villainy sort of came out of left field to me? I mean, obviously it was planned from the start, but I hadn't really gotten the whole "things feel off" vibe that the research team had been discussing- most of the characters seemed to feel pretty free to speak their mind - Kathy openly says she doesn't like the town, Hailey says she wishes there were more people around - and Ben's talk about the environment and deforestation didn't quite give the impression of a philosophy that would motivate his authoritarianism or mass murder- I don't think he even makes any mention of what his vision for the town is, or what his criticisms are of society that led to him forming Brownsville. Obviously he's not going to go straight into "Hey this is Brownsville where I rule over everyone and they're my slaves", but it felt odd to see him go from "Yeah, we both care about the environment!" to "Your being here is proof that the devil is after us" with not much explanation for the change.
The logistics of how the citizens are trapped in Brownsville don't really seem to be explained, either. Like I mentioned, the characters seem free to speak their mind, so it doesn't seem like it's a social pressure? And Ben's the only authority figure seen around town, there's no guards or anything like in Jonestown. One of the letters mentions that they're not given any money to buy food, but three of the town's nine buildings show the citizens in charge of food- the pub and diner serve it, and Michael specifically says he grows most of the food. Not only that, the brothers at the pub even discuss how they have an employer/employee relationship, and if Ben's the boss of the town and not giving any money, it seems weird that there would be any employers in the town to begin with. I think exploring this a little more would help the player share the research team's suspicions, as well as giving the player more of an understanding of how Ben managed to take control of the townspeople and what kind of harm they were living under.
The puzzle mechanics are all things that I absolutely love, but some of the clues to follow them felt a little lacking-
So, starting with Rose's receipt- there's not really anything that suggests the player should look at her bedside table? While "just interact with stuff until you find something" is usually a good strategy for games, Brownsville has a pretty noticeable lack of flavor text- the houses get one bookcase or fridge, and sometimes not even that. (Ironically, the only house with two pieces of flavor text, the yellow text, has one telling you not to go through people's stuff) So now that I'm in the second half, I've kind of got this impression that I shouldn't be just interacting with random objects, because I'm not going to get anything for it- my instinct when I notice Rose is gone isn't "Well, let's poke around," it's "Well, let's search for other people," because that's what's been giving me results so far. And even if I decide to try interacting with things again in the red house, I might end up getting the impression that it's the wrong path, because only the fridge and bedside table will actually do anything.
Obviously adding a bunch of flavor text to the town would be a lot of work for something this small (although it could also be used to flesh out the story a bit), but something simpler you could do would be to just add a line somewhere referencing the bedside table, so that it sticks out a bit more in the player's head. (For example, maybe Rose could tell Sue to make sure she hasn't left anything in the bedside table before she leaves)
From there, figuring out to go to the diner goes smoothly, but I didn't really pick up on the prompt to look in Tilesets- like Dogz, I had figured it was a bug of some kind and that I should still be approaching this like a normal game. And while I don't think that unique gameplay like this has to connect to a game's story at all, I do think you have a nice opportunity to mesh them together here- since the player's researching the environment, and tilesets are the game's way of making the environment, maybe they could make a comment linking the two? (Of course, just observing "the tiles on the floor are all messed up" works just as well, since it's a tiled floor, and that's probably more direct, haha)
After that, though, it's pretty easy to follow the progression! (I mean, I guess you could maybe make the argument that the filename for the cipher doesn't quite say how the cipher works, but it's pretty simple, and it's pretty clear your goal is to decipher the text) I do feel like reading the note in-game could be improved on, though- since the player can't decipher the text without copy+pasting it, having to scroll it is a bit tedious, and the game directly tells you where to look for the file, whereas the other file clues were more subtle about it.
By the way! This is totally just a suggestion, but Dogz made a mention of seeing the files in the game's folder before they were needed in-game - did you know that Essentials actually has methods for downloading a file from the web? So you could literally just run, say pbDownloadToFile("https://media.discordapp.net/attachments/861688372958330903/874877601792016405/title.png","Graphics/Tilesets/Hailey, Jim, and Kathy's portrait.png")
when the player enters the diner, and it wouldn't appear in the game's files until then!
Honestly, I don't think this is necessary at all for Brownsville- people aren't usually looking in the folders you picked, and if they are, they can probably guess when they come into play- I just think it's cool as hell and I think you'd probably put it to really cool use in a future ARG-style puzzle like this!
For the purple house and pub, I was confused as to why you gave them two identical maps to find the notes in instead of just making the note events depend on their switches? It still worked fine in-game, and I don't think it takes up that much more space to do it this way, but it seems like it'd be a little easier to just have the one map.