SKILL SEAL ON NP!!! This is so unpredictable, it's good but it can majorly screw with you! David in particular, who I used a lot back in Onigashima, would skill seal Raikou after his NP, which caused her to brutally attack my team instead of doing whatever harmless buff she would have. I'm happy to say I plan around it now lol, but at the time David was pretty much the only ST NP user I had. Old times!
Unintentionally dangerous skills?
I made a mistake while farming at the Ruins in Part 2 when I fielded
Georgius against Jalter. Normally a tank wouldn't be a problem but his NP is risky since the Dragon trait it inflicts allows the target to receive both benefits of Jalter's charisma skill. The moment I saw her gaining two buffs instead of the single she usually receives I honestly felt baffled but also curious.
I'm wondering if there are any other Servants that have a foe they are ill-suited for due to how their skills or NP interact in unplanned ways.