There's going to be a few of them, so it probably makes sense to start a thread for them.
Here's my first three.
1) If Silas Marsh draws an Innsmouth Look card, and one of the new MH cards is included in his draw, they all say "draw an additional Innsmouth Look card". Does he draw 1 extra or 2 extra as a result of this? (2 seems to be the literal reading, 1 seems to make more sense)
2) If the Agency Institution is in play, when an Ally would be returned to the box, it may instead be placed by an expansion board, to be collected later by an Investigator for 5 clues. If you have all three expansion boards in play, does this mean that - assuming no other "return to box" effects happen - Glaaki's first servant only enters play at Terror Level 4? (I expect it does mean this, but it would be a significant boost to the Agency's effectiveness)
3) If the Miskatonic University Institution is in play, are all its various abilities for "instead of an encounter" options also blocked by Tsathoggua? (I assume so, which would make this institution basically useless with Tsathoggua)