Usually your booked room/dormatory is not allotted to anybody even if you are late in occupying for the reasons of Train Late.
But if Desk officials play foul then you can lodge a written complaint which they Fear and will never irritate you. So do not worry. If you are late and the room is allotted to someone, then insist for alternative accommodation and ask for complaint book. and raise the issue with higher officer. In this case higher officer is Station Master. And still you are grieved then do not hesitate to ask for GRP help.
and...
more... after your tour is over, drop a letter of your experience with irctc and on Govt portal www.pgportal.gov.in > Railway Board with all the relevant information references of your ticket and booking ID Room no. name of officials station name etc etc. In Short Story should be Long. And this is not to propagate the Fighting with Govt but future incidents can be avoided.