In recent past I've witnessed the "Tap" controversy in the concerned forums, mostly in DCW though, but today's Anime episode did clear it a bit.
1) Amanda's room was left neat and clean just like MO of BO.
2) Conan mentions about the still running tap in the bathroom with a "too", after Haibara finishes off how Amanda's room looked like a BO's handiwork, but prior to this they're discussing the ransacked situation of Amanda's room. If Conan considers the opened sink taps in the bathroom as a sign of a clean room then the it's Amanda's if he interprets it as a sign of an uncleaned room, then it's Kohji's.
Personally I think it was Amanda's and Kohji's bathroom's tap was probably turned off, by the person who took away the scissors and the Shogi pieces from Kohji's hand.(Chek's theory)