I made this house several years ago and don't recall any particular issues with the fit of the roof. However, anytime there are complicated interconnecting pieces (such as the way the front wing and bay window pieces fit into the main roof line) things can get a bit challenging. The good news is that since roof pieces are usually not decorated before assembly; they are much easier to adjust for the final fit:If piece is too large:
Use a hand held Microplane Grater to shave down the edges of baked gingerbread pieces (this item resembles and works in the same way as a wood working tool known as a 'Rasp'). If a big area of the piece needs to be removed, you can try warming the fully baked piece slightly just to soften it (I use a microwave for this) and then use a sharp knife to cut the piece to fit. If piece is too small:
A build up of very stiff Royal Icing can help fill in gaps between roof and wall pieces. Once the icing starts to set, you can use a damp finger or cloth to smooth out the icing, if needed. Depending on your overall design, gaps in the roof can usually be covered up and hidden with your roofing material (for example, I generally use Gum Paste for my roof shingles and find this works especially well because the Gum Paste starts out soft and flexible and can therefore be bent and shaped to fit oddly shaped areas if needed).
Additionally, as I noted earlier, since Roof pieces are typically not decorated before assembly, it can sometimes be easier to just 'redo' a piece that just won't fit correctly and can't be corrected by any of the above methods. I recommend keeping some spare Gingerbread dough on-hand until the house is fully assembled.
Sorry about writing such a lengthy response to your otherwise straight forward question. I suspect that the idea of having Gingerbread House pieces that won't fit together correctly touched on some of my most basic Gingerbread House building fears.
Hopefully the above shows that there is usually some work around for the issue.