Without seeing your scene nobody can tell you much. Generally though, it's probably normal. AE's 3D tracker is totalyl arbitrary and doesn't care for things like scene scale or axis alignment. As long as there is a valid camera solve, it's quite possible Nulls end up almost in the same place. all depends on your footage...
Sounds like user error. You must be applying tracking info from the same tracker to different nulls. if you are using AE's Track Motion then you have to track each object individually and change the Motion Target for each tracker.
It sounds like you are new to Track Motion so you should probably type Track Motion in the Search Help field at the top right corner of AE and check out some of the community resources. You'll find plenty of info to get you on the right track.