I know that can happen from time to time. I’ve not personally experienced it but this could be related to your issue? Hope this provides some insight.
https://wordpress.org/support/topic/wp-dashboard-menu-shows-1-plugin-update-but-all-plugins-are-up-to-date?replies=5
Thread Starter
SRD75
(@srd75)
Hmm, I manage a few WordPress websites, and none have an admin caching issue like the one noted above Will.
Thanks for your reply.
Thread Starter
SRD75
(@srd75)
I noted the issue occurred again on a local WAMP site I copied the WordPress files for from my external HDD.
The solution was to replace the files on my external HDD and WAMP site with a freshly downloaded copy of WordPress 4.5.2.
Thread Starter
SRD75
(@srd75)
I take that back. As soon as I refreshed the page, there was 1 update available again, which can’t be seen on the /wp-admin/update-core.php page.