Recently started having problems when using the tool. I'm playing on a server with my friends and when I used the tool on a small stone deposit, desynchronization occurred. Today I used the tool on the Iridite deposit (Space Exploration) and again desynchronization occurred. The server is dedicated on Linux.

Thanks for the report. I released update 1.6.3 that fixes it but it requires Factorio version 1.1.106 (currently latest experimental).

I've also removed downloads for previous 1.6 versions because it's caused by an oversight I fixed for 1.6.1.

What caused the desynchronization problem?

wait... why minimum required factorio version to experimental 106 o.O
does that mean i don't need to update it on my stable server bc is 104 and under minimum req?

What caused the desynchronization problem?

Caching data in local variables from temporary mining drill entities. Players who join later don't get the cached data with the downloaded save file, script has to create their own temporary entity to cache it and causes a desync.