When Troi calls at Clara's quarters to take her to the pottery class, she appears to come from another room and not the corridor. When they leave together, it appears they're entering the other room.
When the kids are playing with the clay and the invisible Isabella knocks over the tray on the table, you can see someone's hand doing it.
Around 27 minutes, after Isabella knocks over the hot chocolate, you see a crewman in gray clothes (or the shadow of actress Marina Sirtis) crawling through the set.
When Troi confronts "Isabella" and Clara tells Troi "Isabella's" threatening response, Clara is clearly scared--and Troi, being an empath, should be able to sense Clara's fear. Yet in the next scene, she acts as if Clara was just acting out.
Isabella is an energy being that trips no triggers. The ship does not detect the presence of an intruder or the sudden jump of energy aboard. Counselor Troi reads no angry thoughts (nor, as was previously mentioned, fear from Clara). Geordi, with his special VISOR that detects otherwise invisible energy patterns, sees nothing out of the ordinary when Isabella visits Engineering with Clara. Guinan, with her own set of special and undefined abilities, detects nothing of Isabella's presence in Ten Forward.
When Clara speaks with Guinan, Guinan mentions that she had an imaginary friend as well that was neither a "he" nor a "she" but an "it." She then goes on to refer to the friend as "he" multiple times.