Then the first question becomes "what reasonable steps would TMP have taken to wake everyone up?", and the next question becomes "how then can this be circumvented?"
On the first, I would expect a given team to be awoken under any of the following circumstances:
1) Wake-up call from Prime Base
2) 5-year timer runs out (timer can be remotely reset by anyone superior in chain of command)
3) Bolthole is compromised
4) If any of the capsules fail*, endangering the crew - this might just awaken the CO and/or medic(s).
I would also expect that members at any given command tier have sufficient knowledge to take command at the tier above in the occasion that this is necessary, but that there are safeguards to prevent a coup (we can discuss this issue later). I would likewise assume that teams have the ability to go back to sleep if they feel it necessary, like, for example, if the area was too radioactive.
As to the second, here is my first stab: Don't assume a screw up on the part of leadership, assume enemy action.
Shortly after the war, before they knew about Krell, Prime Base sent out a coded set of commands to all the teams and facilities - the timer reset code, followed by request for a reply indicating the status of each facility and the success of the reset. This was considered a necessary step to ensure that the system worked and to determine the status of the Project as needed for planning. Unfortunately, one of Krell's hackers got lucky** and captured and recorded the signal, not knowing what it was but recognizing any powerful post-war transmission as important. They were even able to establish a rough location of the transmitter off of the signal, leading them to the area of Prime Base.
During the attack on the base, that same hacker wanted to rebroadcast the signal to see if they could gain some situational understanding of its purpose. Taking advantage of Krell's control of the exterior, he found Prime Base's powerful transmitter and patched into the system, drawing on the base's own power and using it to broadcast the signal over and over again while he monitored the area for a response. His efforts wound up being for naught - the nuke was detonated shortly after, killing him and damaging his patched-in hardware, slowing his retransmit rate by a factor of 2^15. Instead of transmitting every 30 minutes, it was transmitting every 2 years, powered entirely off of the base's own power supply.
After the Krell attack, command tried to wake up the designated backup command location, knowing that if for some reason that failed, the timers would wake up the entire Project in a few years anyway. They failed because the nuke had not only damaged the hacker's timer but also the communication line between the base and the antenna. They attempted to repair the damage and resend, but all died before they could even make it to the site of the damage.
So the result winds up being much the same - the Project made no ridiculous mistakes, but the Project is still asleep thanks to a damaged transmitter hardwired to a fusion plant that resends the timer reset faster than the timer can wake anyone up. For the first century or so, the only teams being woken were due to exterior damage to the bolthole or deliberate actions by groups like Krell and the Kentucky Free State, either of which tended to lead to the destruction of the team. Capsule failure has started to be an issue in the last few decades, but not enough to wake up many teams. The big command facilities were better protected and none of them have experienced any survivable failures***, and prior to the PC team none of the handful of teams to survive their unplanned awakening were able to establish the kind of contact needed to awaken the Project. The bulk of the losses to the Project, besides Prime Base, happened in the war itself or due to predation.
*: Note that surviving the capsule is not guaranteed even if the capsule reports itself to be working perfectly - survival is dependent on the capsule AND the individual. The capsules themselves have many backup systems and an extremely low failure rate, even though some will not be revived from nominally functioning capsules.
**: Going with one of Pixar's admonishments to writers - using coincidence to get the protagonists INTO trouble is good writing, using it to get them OUT of trouble is bad writing.
***: So some might have gotten nuked, but none had a cave-in or capsule failure.
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