(1) EM plant with two different fluid inputs (e.g. EM science) has one pipe system with both fluids mixed after each warp (needs manual flushing). This is very frustrating because it breaks production and requires precious fluid voiding.
(2) Warp train switches to manual mode if it's on the ground floor while warping into the transition.
(3) Warp train errors with "ERROR: Could not find second station for WarpGround" when on the factory floor during the transition. I.e. the train will be stuck on the factory floor, but it will resume warping to the ground floor once warping out of the transition.
(4) "Next planet" display on the top left of the screen always shows the wrong planet or "nil" since the last update.
(5) Researching "Warp repair ground platform" while in the transition cuts the energy transfer between the garden floor (where my power plant sits) and the ground floor. Cannot be fixed, requires a reload.
(6) Researching "Warp repair ground platform" removes hazard concrete from the ground platform.
(7) Upgrading the mod removes some Gleba-specifc recipies of bio chambers on the ground platform.
I consider (1) - (3) critical because they cause quite some frustration.