Can I rectify the completely built dog doors of mine?

You can most definitely can rectify the dog doors. You need not worry as there are always solutions available to rectify the same. You can opt for numerous ways for installing these doors. I can say that the easiest way to fix this is to take the door down, and trim off the top of the door. I'll usually just run the door through my table saw to trim it down, but a power planer would probably work better if you have one. You can also use a hand planner for the same. You need to be very careful while trimming off the door. The rectification of the door majorly depends on the kind of door it is. Try out measures as per the door you have installed. It can either be a ready to use door or the one that you have got customized for your dog. If the door was bought readymade then it is easy to make rectifications in it, more over replacements are available for the damaged areas. But, if you got it customized then it requires greater investment and time to rectify it. Do not worry that you have to start from the beginning. Consult the person who is perfect in the area, there are lot of options available that you can look for the door rectification.