Valna,
In my plant, we are have the same "online polishing unit" to remove the ions from condensate water. Here we do not have any problem with resin carry over. We have a resin trap. So far I have never seen any resin in the trap. There may be a problem in your unit. There is an inbuilt strainer which is installed inside the unit will not allow the resin to come out. It causes major problems.
How you are admitting the condensate in your unit? its from top to bottom or bottom to top? If the flow is from bottom to top, it may fluidize the bed if the velocity crossed the minimum fluidization velocity. If this the case, you check is there any option to change the flow pattern or limit the flow.
If you cannot do anything, you can go for "basket" type strainer. This will take more load than "Y" strainer.