please follow the overtaking rules than guessing
RULE 1).Train with higher speed sanctioned has higher priority
RULE 2).Trains with less travel time has higher priority
logically so correct
further there are certain guidelines to understand...
more...

these rules in case of ambiguity.
a). train must overtake the other train within 10-12 minutes so as not to delay the second train. i.e. for rajdhanis/shatabdis distance of difference may not be more than 25 kms ,e
for superfast distance should not be more than 15 kms
b).For RULE no. 2, there is always a stn .of schedule overtaking. however,if the scheduled overtaking does not take place upto this stn, then overtaking will only be allowed if there is slack time avl. for the train to be overtaken or if it has a scheduled stoppage further and the train overtakes it within the stipulated time..
however if the train chasing has a higher crbs speed limit sanctioned ,it will be allowed to overtake(refer point 1)
Let us follow an example of goa exp and ltt nzm ac exp.(both trains have same speed limit of 110 kmph)
goa exp. has a slack time between agra and gwalior.
as per RULE no 2. ,ac express should definately overtake goa express,but unfortunately it is only allowed to overtake goa between these 2 stn., otherwise it will troll behind till the next slack or stoppage is alloted to goa express.
rail fans may be tempted to ask one intelligent question!!
ac exp is supposed to reach bhopal first, followed by mas rajdhani!!! then why ot is allowed even though both trains have same stoppages!!
logically speaking and following rule 2 ,you are correct.
but let us understand that there is a stringent rule for rajdhani time-table.
with a crs sanction of 110kmph for 22110,it can never cover the distance between agra and gwalior in approx. 1 hrs 10 min. of sanctioned time -table.
this will definately delay rajdhani .
so this is scheduled stretch where ideally rajdhani will definately overtake ac exp.
this explains that what controllers are doing is well justified
kindly comment and raise further queries !!let us see if it fits with the logic