When does the game end - only in the Check Game End phase or when any of the end game triggers take place in any phase?

Thanks in advance.

Only in the end phase, when the check for the game end is made. This does mean that somebody who just got over 50 VP can still be overtaken, both by VP and by dial.

What do you do in the case of people getting the maximum amount of VP (54 if I'm not mistaken) and they then keep earning VP's.

Does that person continue to increase the amount of Vp's they have past the maximum listed amount or do they stop?

This popped up in a game on the weekend between 3 players who had earned more than 50 VP's and 2 who had earned 54, who wins? or is it a three way tie?

54VP is not the limit:

"The length of the track is not a
limit on the number of victory points that
can be earned." (p. 4)

What we usually do is reset someone to the start of the track as an offset from 50 (so if Nurgle gets to 58 points, we put him on the '8' space on the VP track) to mark how far around they get

Wulfen said:

There are some tie breakers listed on page 22, I think the list is fairly exhaustive and should rarely let the game end in a tie. Since the last tie breaker (except for two players reaching the dial victory condition at the same time) can be "highest threat", and every threat value is unique.

Specificially, if more than one player is over 50 VP, the one with the most VP wins, and in the case of a tie, the one with the most threat wins. So the one among the two who had 54 VP who has the higher threat value would win in your case.