If you pull up a special fishing monster on the same pull you were fetching a chest on you lose the chest. (I.E. I fished up a serp with a tmap on it while trying to fish up a mib. Afterwards I no longer got mib loot nor a chest, only fish)
I've never had this issue. I've pulled up serps and shipwreck krackens at MIB spots and upon continuing to fish I still get my MIB chest.
I'm guessing it's an exceptionally rare chance of happening that the serp pull happens on the exact cast the chest is supposed to come up. I've had many more cases where I can continue to fish up mib loot or the chest as you described, just that one where I "lost" the chest.