We tested this with roughly 50,000 markers in three different categories, the plugin behaves as expected.
In order to assist you with this issue we would firstly need to attempt to reproduce this at our end.
If we are able to do so, then we will have identified a bug and will release a patch accordingly.
If we are unable to do so, then there must be a problem of some kind at your end, in which case we would need access to your the site (and potentially the server) in order to assist.
If you’re unable to share the data with us, and unable to grant us access to the site, considering we can’t reproduce the issue locally, the only alternative would be to book a TeamViewer session and allow us to use remote assistance to help. If you’d like to book that then please let us know by opening a ticket at https://wpgmaps.com/contact-us and we will book a session with you.