During WoL and HotS, Amon used Tal'darim as the Protoss ingredient for the Hybrids. This is why the Tal'darim joined Amon, they wanted to ascend. The Terrans were only used because Amon wanted no faction (including Terrans and Protoss) to have control over his production. He rotated from the Confederacy to the UED and then to the Domion. It is unclear if Mengsk really knew about the Hybrids at all.
"Can you hear them, Zeratul? They are coming.", was all Kerrigan said back in WoL. However this means she was involved in the major conflict at that time. Controlling the broods alone would remove Hybrid resources from Amon. Invading the Dominion worlds in WoL now makes a lot of sense. She was probably hunting production facilities. Finally, Kerrigan was taken out of the fold by Narud. By removing her Narud accomplished two things, control of the Swarm and releasing Amon from the Void.
By the time Narud fell the Terrans were taken over through mind control by Amon himself. Facilities were now on his complete control.
Then when the Templar fell on Aiur, he switched to that Protoss resource. Alarak was infuriated by this change of events.
At this moment in time, just after the Spear of Adun escapes, Amon had the following:
- Mindless Zerg Resources
- Mindless Protoss Resources
- Mindless Terran Facilities
Then, the remaining factions were supposed to be killed. Enter Artanis.
I do not see hostilities between Moebius Corps and Tal'Darim as a plot hole. In strategy, I would not like my foe to know that these two factions work together. As well, there are two sides to the Moebius group at that time: Mind controlled and regular Terran Scientists.