When testing for Celiac, doctors sometimes check IgA levels along with the tTG test. The reason for doing this is that if somebody has an IgA deficiency, they could come back with a negative tTG test even though they really do have celiac disease. So it's really done just to make sure the tTG isn't a false negative.
As for what elevated levels of IgA mean, it's a very non-specific measure. It could mean lots of things, or nothing really. But you are correct that it is sometimes elevated in people with autoimmune disorders, so having it elevated a bit in a Crohn's patient isn't too surprising.
See this link for a little more info:
http://www.peacehealth.org/kbase/topic/medtest/hw41342/results.htm