Because two cannot work at the same time and It is like that on global level. You can manage priority by setting index (lower index = higher priority) and applying unique conditions. See how Warmaster overrides Limbsplitter when proc.
I know there is no easy way to put magic effects on enemy hit but using these perks is a bad practise and it even breaks vanilla perks, imagine dozens of mods fighting for priority, only one mod will win.

Hmm, is this the same with OnHit scripts applying spells?

i believe OnHit is different it is a event that is waiting to get passed when its on the queue to be called, now using the "Apply Combat hit Spell" does conflict with other perks

Do all of the Apply X spells doe this? Like Apply Sneak spell?

-MM

Not sure about other entry points but I'm sure that only one Apply Combat Hit Spell is exclusive per weapon hit. A clever use of priority indexes and conditions is required.
For example I was able to circumvent this limitation in my http://skyrim.nexusmods.com/downloads/file.php?id=9419 by adding magic effect I used for new Quick Shot to each of other Apply Combat Hit Spell perk spells (Crippling Wounds and Bullseye). You can do the same if you need to add new magic effect that apply on hit via perk by putting it inside of all existing spells that would cause a priority conflict. You can actually add as much as you like this way by sharing each magic effect between all conflicting spells, it is only workaround at cost of data redundancy. Also note that it might be needed to add HasPerk condition on magic effect defined in the spell in which case you set it to run on target and not on subject.

Oh [censored], I hope this does not happen with "Apply reanimate Spell" too...

Edit: Yes, yes it does
My tests confirm this for the "Apply reanimate spell" entry point, so it stands to reason that its the same for all Aplly X spell entry points. That. Is. Bad....

Edit2: Now implemented the workaround. Thanks mitchalek. I really dislike this though. This just leads to abundant mod condlicts...