Two weeks ago replaced my clutch because it was slipping and when i got into the bell housing i notice that i am leaking transmission fluid into the bell housing through my input shaft. I replaced the seal and everything worked fine untill two days ago. What is the problem.

 

I was looking at it today and noticed that it might be oil i was a little low. so is it possible that i damaged my out put seal from the engine when i put the tranny back in.

 

The pictures I've seen look like the Cummins has a 1 piece seal and the crank has no flange, just a BIG end of the crank and the flywheel covers both.
You can't hurt the seal with the flywheel on.
I guess there's a pilot bearing of some sort that holds up the end of the transmission input shaft and if it gets worn, the input shart can wobble some and might let a little trans lube out.
Everything I own has a little wet area at the real main seal...I don't worry about it unless I see it just dripping or it leaves a half dollar sized spot overnight.