The Soviets encountered heavy resistance from Berlin's flak towers when they were taking the city. The towers had been built to withstand heavy air attack and so even the heaviest Soviet guns were basically ineffective against them. They were among the last places in Berlin to surrender and only then when their supplies began to run out and it became clear that the Soviets had taken the rest of the city.

Even after the war the towers proved extremely difficult to destroy. The "Zoo" flak tower in Berlin took 2 attempts at demolition, one with 25 tons of explosives and another with 35 tons. Many of the other towers were simply left standing and remain to this day.

Given the toughness of the structure, its air defenses, its garrison, and the presence of civilians in a structure that was designed to do double duty as an air raid shelter, any mission like that depicted in the video game would have been extremely foolish.

The only references I've seen to an internal explosion in one of the towers (outside of the demolition attempts) was one of the towers in Vienna. The only information I was able to find about the cause is a German language website which says that it happened in 1946 due to kids playing with abandoned 125mm shells.