I think I understand what you want, if so, you're using ismember the 'wrong way round':
function real_time = time_from_videos_to_second_convertor(time_data_observation_entry, frame_rate_played_video, real_time_vec,frame_vec)
frame_id = floor(time_data_observation_entry * frame_rate_played_video);
[found, where] = ismember(frame_id, frame_vec);
assert(all(found(:)), 'Some frames were not found in frame_vec');
real_time = real_time_vec(where);
Note that I made the above function error if a frame is not found in frame_vec. Otherwise, I'm not sure what you'd want to do. You could set the corresponding entry to NaN or remove the entire row. It's trivial to do either.