Conceptually all transactions in the block chain lie on a single timeline. The fact that we quantise that timeline into blocks is in many ways neither here nor there - it's still a strict line. 

What can happen and you must be aware of is duplicated transactions. Satoshi sort of assumed this could never happen because everything is hash based, but forgot that duplicating coinbases is possible and at one point this did happen. It was banned by a rule change afterwards but you still must be able to process the older parts of the chain that have this. There is a BIP that covers the new rule.