Some stress could certainly attribute to it. It’s a shame we have to separate them but it’s for their own safety if they are getting hormonal. I fostered a pair of girls who were able to stay together from babyhood into teenagehood. There was a bit of dominance mounting but it never escalated into fighting.
Poop pics are useful if you have any to share. It’s not uncommon here on BB. Lol I wish I had taken some of what I saw earlier today as it sounds like what you are describing. This from a 6yr old bun that’s always overproduced cecals and has some ongoing health issues. There was thumping going in there room last night so Im also wondering if it’s some post-stress poop.
Tweaking the diet is certainly something that you could try. It may be that one got less when they were sharing, but now is getting more and it’s thrown things of a bit. At their age, their gut is changing too, so you may see some anomalies in the poop department. What type of hay do they have? Maybe cutting back pellets for a bit and encouraging more grassy hay will help balance things.
If they are getting more frequent or more loose, definitely visit the vet. It’s also an age where you may see some presentation of intestinal coccidia or bacterial imbalance in the gut.