[Michael.Ante]

What is your read-length distribution? The older versions of TopHat had problems, in case of too high length differences. Additionally, reads below 20 bp are very hard to map; I discard all reads below that length (denote you need to control for the pairing information).
Otherwise, you can try a different aligner (e.g. STAR or bbmap).

[colindaven]

This was troublesome for me as well.

Using the program bamtools helped no end ! Detailed in this post:

https://www.biostars.org/p/88582/

It looks arcane but it's worked for me on thousands of samples. Hope that helps.