That is definitely part of the problem - however every time I defragged the indices, some were over 90%.
Personally, I don't think high fragmentation should be a critical problem for some databases - just a warning. The database still works fine, it's just performance is slightly down.
I've just found it's possible to change the % fragmentation that generates a 'critical' on each database, so I'll be amending the limits on some of my problem databases, which will make it much more useful.
It's just a shame I've got one or two other badly written applications that cause other alerts (high page splits etc.)