Here's the biggest issue with the timing of the story, the Punisher actually joined up with the Thunderbolts WHILE PUNISHER: WAR ZONE WAS COMING OUT!
So while he's being locked up in a super prison, he is being recruited by Thunderbolt Ross to join Ross' new team of ruthless heroes in Thunderbolts #1 (by Daniel Way and Steve Dillon)...
He runs into Spider-Man a month or two after Punisher: War Zone (during the time that Spider-Man's body had been taken over by Otto Octavius) in Avenging Spider-Man #22 (by Chris Yost and David Lopez) and it wasn't like it was weird that they were meeting up with each other again...
Heck, there was even a two-part story around this time by Marc Guggenheim, Leinil Francis Yu, Mico Suayan and Sunny Gho that involved the Punisher turning himself in and getting arrested so that he could be at a court room when a vicious killer turns State's Evidence was testifying!
So, in other words, obviously he DID escape that super prison, but we never actually got to learn how. Apparently the big bad super prison that was a major plot point of that miniseries really didn't matter either way in the end.
Thanks to Luy for the suggestion!
If anyone has a suggestion for an unresolved comic book plot, drop me a line at email@example.com!