I suppose I should mention the Companion Drone does not warp with you in Warp Drive Machine.

I mean it does after Nauvis, So I suppose its just because Warp Drive Machine nukes all entities on Nauvis when warping

Hello,
I'm lost with your description. Are you talking about some other mod? The Warp Drive Machine by MFerrari?
If so, cross-mod compatibility is possible, though it's pretty hard to do- if at all- depending on how both mods function.

So I went out to scout this bug anyways (because the only Warp Drive signature I found is the mod by MFerrari) and I tested it with Warp Drive Machine and found the problem. When the ship warps, Warp Drive Machine copies everything standing on it to the new place, and a companion that was on the ship got copied too. The copy looks like your drone but does nothing, while your real drone follows you. Only the basic Atlas was safe from this.

The fix ships with version 2.5, which releases very soon: your companions will step off the ship before the warp and join you again right after it, so no copies are left behind.

If something still looks wrong after the update, please tell me what the drone was doing when the warp happened. Thanks!

The new 2.5. update is out. You can now test it if it works well. Thank you for your report <3