ToME: the Tales of Maj'Eyal

First if Time-Prisoned critter is hit, his hp doesn't decrease (that's correct), but in the message window I see line"X was hit for Y damage"
Second - time prisoned monster can still cast spells - mountain troll cast lightning on me, and can be stunned while time-prisoned
PS could be mountain troll problem - he cast lightning while stunned too

Is he casting lightning or are you getting hit with his thunderstorm?

Time Prison prevents NPCs from acting. However, the damaging "auras" still work: Thunderstorm, Chants, Hymns... Mountain Troll Thunderer is surrounded by a lightning aura, so if you hit him, you still get hurt by that aura.

I didn't hit him, I was not even close - several squares away

Thunderstorm goes off every turn and can hit you up to five squares away regardless of rather or not you're damaging a creature.