Today I downloaded a couple houses, then after moving in a family to one of them, I noticed they we're barely interacting with anything, or anyone, free will is on, and they will do stuff, but mostly stand around, including visitors. The household has 8 sims, so I initially thought my game was glitching due to too much cpu being used from a large household (which I've never encountered with sims themselves in ts2, just bad lag, and it usually takes a bit more than 8) I went over to another household, only to run into the same issue. Next I thought I may have downloaded something from a file that messed with their activity, so I put all the new cc into my folder for sorting new cc, and went over to sims 2 Clean Installer to isolate any red, or pink mods, only 2 behav mods came up, which are ones I've had for awhile. So now I'm at a loss on what could be causing this issue.

Do you have testing cheats on? If not put it on and see if you are getting errors. One thing that can cause constant errors are chimneys, so check if these houses have chimneys and try replacing or getting rid of them entirely.

I have testing cheats permanently on, but get no errors.

Did you add anything to the lot that has moving items? Bushes with custom butterflies will cause lag.

Might be a case of doing a 50/50 if there are no clues.

I haven't, and this happens to all my families, I have tested out a couple others.

Maybe you have a very attractive object on the lot with an interaction that doesn't work right. It could be a reaction emitter with function - awareness. They almost always want to use this one obejct, the action ends immediately, then they wait a bit and repeat it again. In this case you might see an action icon briefly flashing in the queue. Does it happen on an empty lot?

Nothing lines up in the queue, 90% of the time it's just of them standing doing nothing, almost like free will is off, but I double checked that it's on, and they still do stuff, but scarcely.

What I would do is to backup and then test the neighbourhood with your Downloads folder removed (be sure to make a safe copy of the neighbourhood, as you'll want to restore it after testing in case removing mods breaks something).
If the sims behave normally, you'll know it's something in your Downloads folder.
If they are still inactive, then test with a completely new neighbourhood, if this works then you'll know it's a problem with your lot or hood.

You could run one of the hack conflict detectors before doing the 50/50. I don't see that mentioned. But after that I would be making a full back up, pulling all downloads and testing CC.

So I had to get off the computer, and only half made the family, I moved in the rest later that day, the problem started when the rest of them moved in, and I put them in a new house. I'm not sure if it's the other 4, or the house, but I moved them out, and then I moved the first four onto an empty lot, and they seem normal, I'm fixing to move them back to see if it was a conflict with the others, or the house itself. But the neighborhood is working fine.

Final update, I moved one of the new 4 into the place where the og 4 were staying, that sim stood around doing nothing, I moved them back out, thankfully it did not affect the og 4's autonomy, so I moved them back into their home, and they have been fine since. However with the other 4, I'm not sure what went wrong with them, but none of them ended up acting right, so I killed them off.