How to fix the issue?

You need to modify the system.yaml of the Xray, to increase the limit for the numbers of the files with the same SHA256.

The Xray system.yaml is in $JFROG_HOME/xray/var/etc/, and you need to modify the following snippet, to increase the default value.

server:
    # default 500 
    scanMaxFilesToCheckPerSha256: 1500

The Xray must be restarted after the modification.