When a defect should be logged in agile ? when found or at the end of sprint?

Could someone give some feedback on the fact that what is the right time to log a defect in a defect tracking system in agile .

If we log it right when we find a issue , it might flood the issue tracking system with a lot of issues . On the other hand , if not logged , it is very hard to track the issues .

Please give me some context on how you use that in your team and what are the best practices.

Thanks