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I have a breeding pair of convicts in a 40 gallon tank,no other fish in the tank. Both are probably a year to year and a half old and they have been in the tank together for around 6 months.They have breed a few batches of fry,last around 2 months ago. They have always seem to have gotten along fine I have never noticed any acts of aggression between them. When I came home from work this evening and went to feed them however I discovered the female hiding at the top of the tank behind the filter tube some how as if she has now become afraid of the male and is trying to hide from him.Does anyone have any idea what the problem could be and is this something I need to worry about? Thanks ahead of time for any responses.

Just one of those things that can happen sometimes. If he started to see her as a threat to the fry it could trigger an attack.
I would try redecorating the tank or maybe add a few more caves for the female to hide in.
Failing this divide the tank until they are ready to breed and/or the male starts to calm down a little bit.

Totally agree - anything can trigger the male to 'turn' and due to the difference in size, she is going to lose out. Personally, when this happened to me, the only thing that worked was to re-house the male in a larger cichlid tank for a while to 'put him in his place' - then returned him (moving all decor around) with female. Resulted in many more broods. Hope your situation improves.