Yup. Someone probably tied two circuits together somewhere and the ended up on the same phase. It may
have been that way since it was built. I've seen it more than once
You need to
A) disconnect one wire and clearly lable it as "backfed from circuit # whatever"
B) map out the circuits and start taking stuff apart, find out where the cross up is and disconnect/label it.
EDIT. OK. Forget that....new info.
Wires to breaker are red and black-
Find the "homerun" jbox (the first box after the panel). The circuits are probably tied together there. Split them up and put the red/black on different phases!!
(not on one tandem breaker)