I just started a new game, and picked him up ASAP in the Copper Coronet.

I went to rest, and before resting clicked on his spells to choose them. This is when I noticed that he is Level 11!!! He's always been level 8 when I pick him up!

Is this some sort of bug? Will it have an adverse effect on the game (besides things being easier with an undead turning machine)?

All the characters come at different xp levels depending on yourself and your party but it's no bug.

The level of NPCs who can join party are determined by the highest level which occurs in your party. There are determined steps of NPCs levels, and they have maximum. In BG1, this is 6th level, in BGII 12nd, and if I remember correctly, in ToB this is 17 (So if you come to pick up Anomen with a 25-30th level party, he will still be 12)

I was level 8 when I got him. Jaheira and Yoshimo were also in the party. Jaheira was 7/8 (I think) and Yoshimo was level 10.

We went straight from Irenicus' dungeon to the Copper Coronet.

In every other game, Anomen has been an 8th level Cleric. This time, he was level 11. I don't know why.

Did you bring Minsc and Imoen with you? What class are you playing? Some classes can reach higher levels at less experience than others, and one less NPC would have meant much more experience for everyone else.

I was using "Dungeon Be Gone" and only brought Yoshimo and Jaheira with me.