As said below, it happens twice more in the series and once more in Generations.

It was originally intended to be regular, but it proved to be too expensive too regularly film new footage for it, so it would have ended up like Power Rangers, where every single time they reused the exact same footage, which breaks the audience immersion. But perhaps more importantly, if the ship separated during every emergency situation, it tended to pause the action, and eat up time in the episode, which affected pacing.