"Last Import" in Photos shows 1,000s of photos, not just last import
You could try rebuilding your Photos Library. However, ensure you have a backup of your Photos Library (e.g. a Time Machine backup) before rebuilding the library!

To rebuild the library, follow these steps:


Make sure that Photos is not running
While holding down the optioncommand keys, launch the Photos app
The Repair Library window should appear
Click on Repair to rebuild your photo library


Depending on the size of your library, this may take some time.