It's actually not all that uncommon for strips to be altered when it's reprinted in book collections. There's a chock full of those in Bloom County.
It seems that Bill Amend's FoxTrot is no exception.
First off, this strip, which appeared in papers (or at the very least, The Deseret News)
Here's the version seen in the book collection:
Probably the biggest change is this one. I found this in an internet message board discussing comics:
Annnnd this is how it was reprinted:
And here's a more recent strip, from 2000 (the above two are from 1989):
In the book collection, Andy's line was changed to "I thought Bill O'Reilly seemed a little soft-spoken"
I think you can guess why the final strip was changed.