The attached screenshot demonstrates a talk with Yahota over Navcom which was made few seconds before taking the screenshot. She says she's here, but walking on every available spot of this small top of the tower area does not spot her anywhere. Also, another talk - exactly same words spoken - was made few seconds prior to entering the top of the tower.
Quests-wise, this happened after getting the thing in the mutant dungeon, opening the big old ruin in the camp, talking with professor after he went down there, then sailing around a bit, getting the messages and quests to investigate Nexus of Technology and Horticulture Center (which quests are still active and not completed), going through the former, sailing around some more and getting the message about professor being kidnapped, and then going back to the Expedition camp. No interaction with pirates whatsoever - nor with their spy in the camp - were made. Also, no interaction with Yahota after doing 1st (mandatory) camp defense - the tower stood closed all the way till "now". I.e. pretty usual going with Expedition quest line.
P.S. I conclude, assuming she's not lying to me, that she's indeed on top of this tower, but she's currently in some higher dimension, which is why it is impossible to detect, or bump into, her.
