The fresh foods are designed differently to the frozen ones. Whereas some may be pretty much identical, a fresh pizza may have a different dough to afrozen one that wont cook properly straight from frozen, or a fresh lasagne might have a differently designed pot to a frozen one that allows the heat to transfer differently.
Generally, it's just to cover their backs, and cooking it a bit longer, or chucking it the microwave for a couple of minutes first should sort out the problem.