I'm not sure what you mean - are you saying that if a call enters the IVR at, say 2:59, they get the "with callback" schedule, but by the time they hit the callback node it has gone past 3:00?
In this case, you could either adjust the schedule to finish a minute or so earlier (depending on how long it typically takes to reach the Callback node), or you could use a Logical Transfer node, with an expression based on time, immediately before offering the callback.
I would suggest that the former is probably easier.
HTH