This is a fairly common issue. It happened to me two or three times already and I know several other forum posters experienced it too. From what I can tell, it happens some time after you re-allocate passive points. In my latest case, I completely filled four passive trees for a seasonal challenge, then reset all of them and re-allocated them slightly differently. After a few missions, my passive skills balance was negative. I think I levelled up while doing the missions - this might be the point where the passives count gets messed up.

It might be the server is incorrectly using a previous snapshot of your skills and combining it with the re-allocated ones, so you end up with your old build combined with the new one.

The only solution I know of is to use mind reset and redo your tree(s) from scratch.