Re: Neat sim always uncomfortable

@SianAF148 Unfortunately situations like yours (roommates, pets, multiple sims that are not neat, etc.) would probably be set up for frequent if not constant discomfort for a neat Sim. You mentioned several factors that can cause this, plus there are others. Does your Sim go in and clean the areas? That can be one up-side of a neat Sim, though they are unhappy until they are fully cleaned. Some additional things you can try &/or check for are:

• If you get a maid, butler, roomba, &/or Servo your chances are higher that they will catch things you don't on clean-up, and do it more regularly - sometimes before the Sim gets uncomfortable.
• Move around and check under items in the rooms. There may be surfaces that are not visible that Sims have 'stashed' trash or cluttering items that are unsetting your Sim even though you cannot see them there. If you find such a surface it would be good to un-block the area so it can be seen and fixed if it contains something dirty or messy in the future. In the past Electronic items placed while MOO is enabled would cause the surface they are on to be useable to the sim - including for laying trash/dirty items... and you would not see them. In that case you had to re-add the electronic items with MOO not active to stop the issue.
• Somewhat redundant of the above info but I would also check around the rooms for if there are areas that are prone to clutter/dirty items by the other Sims and see if there are any tweaks you can make to the layout of the room to avoid these.
• I would definitely get the self-cleaning litter box for your Sim home in this case. A normal litter box with 3 cats could be a big frustration for a neat Sim.
• Do you have a pet toy box for the cat toys? Toys left on the floor will also bother a neat Sim. With a pet toy box they can be put away.
• You could try riddling the areas with moodlet items to see if this helps counteract the moodlet sometimes perhaps several of the painting inspirational lights or something (Make sure to enable the moodlet on the items). You can find these by enabling hidden objects in build mode.

Anyway, those are a few thoughts. You will probably have to just live with a fair amount of discomfort for a neat Sim in a communal situation, especially with roommates. Roommates are known for being bad some behaviors like this. Fortunately you can 'train' them a bit with encouragements and some other means. There are some roommate tips for doing this  on this page: https://sherigr.com/gameplay-tips/roommates-sims-4/