The contents of a profile retrieved depends on the contents of the organization. For example, profiles will only include field-level security for fields included in custom objects returned at the same time as the profiles.
This may sound unclear what it actually means... Well, basically if you don't deploy a component along with the profile, the profile info will have nothing (permission wise) about the component. You might see an error like this with ANT:
Error: profiles/BIT.profile(BIT):Permission Create Fund_4Case__c depends on perm
ission(s): Read Fund_Detail__c
The reason that the dependency item is missing could very well be that you simply didn't include that dependency item in the deployment package, even though you really shouldn't have to as there's no change to it. This poses some challenges when managing a profile deployment, do you really want to deploy everything a profile may need to use just so as to have all necessary permissions get across? It just sounds a bit dumb to me.