This is usually caused by extension conflicts or settings issues.
Common solutions:
Try opening your wallet manually to see if the transaction is there.
Sometimes the wallet pop-up opens up in another browser window behind your active browser window. Minimize your current window to see if this is the case.
Check your wallet settings and disable auto-lock or set site permissions to "all sites".
Disable other wallet extensions temporarily and try again.
Clear your browser cookies and try again.