See this will not create a lot of trouble. But you can be asked justifications like why you don't have the permanent details on your aadhar card and other details. So you can answer the truth. But this will not create much problems. Until and unless you have discrepancy in your marks or your name then you have nothing to worry.

To know more about JOSAA counselling visit the link below:

https://engineering.careers360.com/articles/josaa-counselling

I hope this answer helps. All the very best for your future endeavors!