In justifying its first raid, Israel said that underneath the hospital lay a complex network of tunnels, a central command center for Hamas. Evidence produced from that raid— caches of weapons, a tunnel leading to small, rusty quarters that appeared out of use, and no scores of militants found — fell far short of the claim . Hagari said Monday that the intelligence had been wrong and that Israel had tipped off Hamas militants at Shifa by announcing its attack plans.
“They left there because they knew we were coming,” he said. “And this time, we did something else.”
By doubling back to Shifa in mid-March, he said, forces surprised militants who had regrouped inside.
He said the military now believes militants operated mainly from the hospital wards themselves, not tunnels underneath.
Apparently they weren't using those tunnels now.
https://www.nbcnews.com/news/world/gaza-prison-doctor-accuse-torture-israel-hamas-war-rcna159710
Also, the hospital chief has some things to say as well.
...Hamas was conducting raids from the hallways and offices of an active hospital in a war zone?
The point I was making is that the Israeli official position changed. They said they needed to attack because of an active base in the tunnels. There is no evidence of a base in the tunnels. They found a small weapons cache! Yes, that makes sense, they were treating wounded people in a war one, some of them would would have weapons, which would need to go somewhere.
When Israeli forces took the hospital, there was scant evidence of their position. If there was good evidence, we would have definitely heard about it. I can only conclude that Israeli intelligence was either wrong or lying, barring good evidence to the contrary.