You basically encountered a bug which is existing since vanilla ME1:
Multiple reports indicate glitching at the transmitter scenario, where the ultimate effect is that of the journal failing to update and rendering the assignment unable to complete. Conflicting reports abound on the causative element of the bug, although the common theme is that trying to damage the tower regardless of method used (weapons, grenades, talents) may cause it to "disappear". Thus, the only expedient recourse is to load an earlier save when this happens. Source: https://masseffect.fandom.com/wiki/Feros:_Geth_in_the_Tunnels
I also ran into this bug myself, but fixed it with loading an older savegame before I went down into the tunnels.
Do not expect any fix in the LE of ME1 for this.
