Answer to the question is 'No, it doesn't affect'

But the detail in the question ' I have two backlogs in my Engineering but I'll still get certificate that my degree is completed.' makes me wonder. How does one get degree certificate if there are backlogs pending to be cleared? So, let me elaborate.

Its ok to have backlogs as long as you clear them before you get admitted for M.Tech. Number of previous backlogs does not count. Even if you have backlogs(result awaiting) while you go for interviews, thats fine as long as you are sure that you'll pass these subjects in the meantime and that you can get at least a provisional certificate to produce during admission process at IITs. Confirmation of your admission offer is subject to you producing all the relevant documents. If you fail to do so within the stipulated time, your admission offer will be revoked.