Ok...now it is more clear what you did
You need to set the opening as Room Bounding as well... Then you do not need a separator.
Same like doors and windows... They are openings too. If you uncheck their room bounding property the room will be not enclosed anymore So make sure the opening has that property checked.
if it's not the opening it can be an offset from the base level you are placing that room on...example the opening not touching the level, or wall has bottom offset, or a gap between wall and the opening not matching properly...in other words the room space is leaking
again assumptions...can't identify the exact wrong step you made without sufficient info or the model with the offending element
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