This happened to me the first time I used glue and it was Elmer's washable school glue.
I guess my glue was a bit old and had thickened. So I diluted it with waster and it
was so much better. I was also told to put the batting down, put the glue on the
batting and then glue the top or backing whichever side you're doing...then do the
other side again putting the batting at the bottom. Use fine lines and if you see
a big smear just wipe it with your finger. I keep a wet washcloth next to me
while I'm doing this so I don't have to run to the sink every time.
Having said that some put the glue on the fabric side and doesn't seem
to have any problem. I guess it's a question of how much glue you're using
and how fresh your glue is.