When a AE2 Block touches a IC2 Classic block and you break and replace the AE2 Block IC2C will start voiding/duping things.

This is due to a new performance optimization not being supported by Applied Energistics 2.
They are aware of it, and choose to not support it.

Why does this happen.
Forge allows to cache Capabilities now and get a callback if the capability for whatever reason invalidates.
This allows to performance optimize since you can now "Trust" Capabilities.
AE2 chooses not to call the callbacks.

Fix for the user:
If you break and replace AE Blocks, just break and replace the ic2c block too with it.

Note:
All Planned AE2 Specific compats were canceled due to this willingness to not support core essential features.

Hotfix

Looks like another dev was pissed off to provide a actual fix for this xD
BEST MOD EVER!
https://www.curseforge.com/minecraft/mc-mods/aecapfix

Images:

When First Placed:

After Breaking the ME interface:

After breaking and replacing the Tube:

Also ME Acceptor has a bug with FE... Not a IC2Classic issue.
Flux Generators work with ME but only the controller. You need a "FE" transport mod to make it work.