No there is no issues with backlogs while applying for GATE ,what the eligibility criteria includes is that you must possess degree  in engineering it is bachelor's degree in Engineering or you must be in the final year of engineering course nothing  more than that. There is no minimum percentage required to appear for GATE.

Hiii

You will not be disqualified or not allowed to appear for GATE exam because of any backlogs but yes be informed that you will have to upload the marksheet of final year incase of backlogs.
The eligibility criteria set for GATE exam say 
"Candidates with backlogs (failed subjects) in any of the subjects in their qualifying examination had to upload a copy of any of the mark sheet of the final year issued from the institute where he/she was studying. It has to be noted that internet downloaded mark-sheet will not be accepted under any circumstances."

If you fullfil all other criteria then backlogs will not cause any hinderance to you but you will have to clear all backlogs in the prescribed duration that will be given .

You can refer to the following link for more precise details
https://engineering.careers360.com/articles/gate-eligibility-criteria

Thanks!!