I don't think Flandre did something bad, just that Remilia freaked out when she approached her from the behind and put her hands on her.
Honestly, if your crazy loli sister with immense destructive power sneaked on you from the behind and touched you suddenly, screaming is the first thing anyone would do.
*CRACK*SNAP*POP**massage**massage**stare*Yes, it feels good. Chen, you are really a good child, aren't you.Ran-shama, does it feel good?A~h Chen, having you massaging my shoulders for me like this really makes me happy.If you can, there's another place I'd like you to massage...AAAAAAAAAH!!