I have the lower leg twist set to zero to stop the seperate parts from twisting into each other so I think that might be a part of it
Other than that everything looks lined up to me. The bones attached to the legs are pistons btw.
This issue started happening to me as well as soon as I updated from VRChat’s SDK 3.7.0 to 3.7.1, and so on.
I’ve tested it across multiple models that have worked previously (all of them being avatars made prior to SDK 3.7), and they all have this same leg issue. Have talked to a few friends about it, but I or no one else that I know have figured out the issue yet. Unless I haven’t look hard enough, which is also possible. 
Have you made any progress on it yourself since you’ve posted this?
11-19-24 Update: Posted this late at night yesterday. It’s been nearly 20 hours, and I’ve found something of a ‘fix’ for the issue, and that’s using franada’s GoGo Loco prefab. If you don’t know what that is, it’s an addon you can add to your avatars that’s suppose to improve it’s locomotion and allow you to do certain poses, animations, even flying, and some other things as well.
I recently applied GoGo Loco onto an avatar of mine that had this leg issue, and when I went to playtest it, it automatically fixed the leg issue. Since GoGo Loco is designed to basically replace VRChat’s regular standard locomotion, I would naturally guess that’s how it fixed the problem on my end. At the cost of adding more space to my avatar of course.
And since GoGo Loco is such a popular addon to most avatars made today, it seems nearly nobody else seems to be posting this issue. Only other post I could find online regarding this same exact issue was on Reddit, and the forum was posted just 4 days ago. As of writing this I still don’t know of an actual fix without using GoGo Loco. But if you don’t mind putting GoGo Loco on your avatar, (which I recommend as it’s almost a must-have accessory for most avatars now.) It seems to fixing the issue, at least for me- across multiple different avatars.
Here’s the link to that reddit post btw…
https://www.reddit.com/r/VRchat/comments/1gs4cvy/avatars_leg_screwed_up_in_play_modein_game/?rdt=49416
11-20-24 UPDATE: After helping out a friend with one of his avatars who had the same leg issue, I discovered something else that’s pretty important regarding GoGo Loco. I learned that the most recent GoGo Loco package does not appear to fix the leg issue. As of writing this the current version is 1.8.6. The version that I was using that fixed this issue was version 1.8.3. I tried testing this on my end twice, and found that the older GoGo Loco version would fix the leg issue, but not the newer one.
This is probably as far I’m able to go as far as figuring out a ‘fix’ for this issue. If anyone else knows how to go about this issue, please speak up!
That worked for me, thank you.