Ok to sum it up I'm only 4 months into my fur babies I have a male about 1 1/2 years old and a female just under 1 year. They bonded immediately and have been living happily together for 2.5 months until tonight I noticed her hiding from him and being very aware of him. I took her out and she was normal with me and just chilled in the hood of my sweater, I usually take them out together but he was on his wheel doing his thing. When he was done I went to pick him up but when he saw her he backed away. So I put her back and took him out and he was acting very jumpy so i figured I'd put him back in and as I did she went and hid and he went back in his pouch. She was staying hidden for 15min or so, that's when I decided to put another pouch in the cage and she bolted for it. What's going on!?!?!?

Is the male neutered?

could be in heat, maybe.

We have at least 2 pouches per cage. the 3 colony likes to sleep together all the time, one glider was added to 2 when we got them.
Our colony of 7 sleep in all different arrangements, mostly all together but at times the sleeping 6 and 1 or 4 and 3.

No the male still has all his plumbing

Most likely in heat then. Keep an eye on them while they're together for fighting or dominance issues (make sure the girl can get to food at water and has a separate place to sleep), and be prepared in case you end up with babies!