They could just be concerned you are going to cause trouble due to the fact it won't "look correct" once it has gone through the C41 process.
I wonder if something similar to, but importantly different than, this may be at least part of the reason for the widespread belief that cross-processing E-6 in a C-41 machine will damage the chemicals. Specifically, because the resulting prints from the slide film's negatives don't look "right," the owners/operators may think their chemistry's been messed up. If said owner/operator immediately shuts down the machine and replaces the chemicals in order to avoid problems, that'll solidify the idea that the slide film did actual harm. The next roll (of C-41 film, of course) through the machine will have normal colors. If my hypothesis is right, several common cognitive errors, such as confirmation bias, are going on in the owner's/operator's head. The result could be a powerful but incorrect belief.
Of course, there could be other factors, like exaggeration of legitimate concerns, heard via word of mouth or in publications. about shifts when doing heavy amounts of E-6; or confusion of ECN-2 film with E-6 film.
They didn't even question it. 
