During the UFO invasion 3 Interceptors, each carrying one missile, go to battle; yet there are 4 Interceptor kills.
When the UFO attacks the freighter, its main compartment is destroyed, blowing up completely, but then it cuts t a shot of the ship's radio still transmitting.
The moon base's ground missile launchers while traveling make sound as if they were powered by diesel engines. A diesel engine requires abundant quantities of air to operate, which is not naturally available on the moon. Even if equipped with air tanks, a diesel engine would be extremely inefficient way of propelling vehicles on the moon, not to mention that SHADO boasted state-of-the-art technology.
Straker and Foster are communicating with Skydiver while wearing diving gear, but the "bite-down" oxygen mouthpieces they are using would make speech impossible.
When the freighter is being attacked, the sequence "Get somebody onto that fire! Is he alright?" is said once but then simply repeated from tape.
The UFO underwater base has not been noticed by SHADO nor the passing freighter (which can't see it and is only on the surface anyway etc). Yet the flying saucers attack the freighter, and use very distinctive weapons, presumably to prevent it from potentially discovering the base when it had no realistic chance of doing that anyway (being only a freighter and on the surface when the base was underwater). So a rather short-sighted move which inevitably then brings SHADO searching underwater for any UFO base since suspected of sinking the freighter - SHADO then finding and destroying the base. (The aliens have already done the same thing in an earlier episode instead just ignoring a harmless passing freighter and which again leads to their discovery and destruction).