I have also been having nearly this exact issue.
General (For all issues)
What device type are you on? iPad Air
What version of the OS are you running? iOS 9.3.4
What model is the device? MH182LL/A
What is your PFID#? None?
Gameplay
Is pass & play on? Is permadeath on? No and no.
Tutorial, Story Mode, or Quest Mode? Story mode.
Characters in Party Kyra only
Location of each character Has happened in all three locations over multiple attempts
Turn Order Kyra is the only party member
Scenario & Scenario Difficulty. If on non-normal difficulties, which wildcard powers are in play? Foul Misgivings, Heroic difficulty, over multiple attempted games with various wildcard powers. Most recently, Retaliation
What card was encountered when the issue occurred? (Or check, or card just played, etc) The Skinsaw Man
Did the issue occur on the first explore or a subsequent explore? If subsequent, what card did you last encounter? What was its resolution? (IE, you just encountered an enchanter and failed the check, and on an additional explore you ran into a blessing of the gods but didn't auto acquire it) First explore of the turn.
Did other characters aid the check? What did they use to aid it? There are no other characters in the party.
Was the encounter a Horde? (Skeleton Horde, Goblin Raid, Zombie Nest, Zombie Horde, Garrison Location Power w/ multiple characters, Henchmen encounter in Black Fang w/ multiple characters) When he is encountered in the Warrens, a random monster is placed on one of the other locations (generally Foxglove Manor because I tend to close the Farmhouse first), but the issue happens whether or not The Skinsaw Man is encountered in the Warrens.
When I encounter the Skinsaw Man, regardless of whether a monster is placed in another location because he was in the Warrens, he tends to do between 10-15 damage to me before any dice are rolled. Then he gets the bonus 1d4 for my being alone and I am given two checks (generally with an empty hand now that I've taken so much damage). Sometimes (I can't tell if there's a trigger for this part or not), the difficulty of his first check is increased by the amount of damage he did to me before the encounter started.
CORRECTION: I believe my perception may have been skewed by frustration. Upon much further experimentation, this seems to only actually happen when the Skinsaw Man is encountered in the Warrens and there is another location open, so it appears to be tied to placing a random monster in another location.