Incomplete fixation, overprocessing, too hot paraffin could all contribute.
Also, a gentle processing with 50 - 60 %, 70%, 80%, 95% x 2, 100% x 2, clearant x 2,
paraffin x 2 or 3, but shorten times/ 1 hour per station (you did not say? time)
could be too much.  Mouse brains are not that huge.   

You also did not say fixation time?  Oversoaking in ice water will also cause mouse
brains to explode on waterbaths, they cut but explode.  

Gayle Callis