I had this happen twice where I would be in the Balmora mage's guild training conjuration by summoning a scamp twice and then resting, and I would do this in quick succession, and suddenly my character would be able to levitate forever. Casting levitate would not fix the issue, either.
I do note that I use levitate as a faster method of foot travel constantly while playing, and I am not sure if that might be effecting things.
That sounds like an engine
That sounds like an engine bug to me, like the one that happens when the game doesn't notice a character leaving water and then the character slowly swims on land. The water issue can easily be fixed by diving into water. I have no idea how to fix your issue, except for not doing what you're doing.
The best way to train conjuration is by a custom spell anyway. Just create a spell "summon skeleton for 1 second" and then you can cast that until your keyboard breaks. No need for resting in between casts.