They trigger "match" coverages that aren't exactly optimal and can expose serious vulnerabilities in your deep shell.
If you run one of the stock 3 deep blitzes (they all feature seam flats) and the offense is in a 3x2 set your defense converts to man coverage on the two receiver side. They maintain their zone assignments on the three receiver side.
Either one of the man defenders could get torched with no help behind them. If the offense gets time then anything crossing from the 3 receiver side to the 2 receiver side will be wide open because those defenders are in man.
For the concept to work at all you need both fast pressure and both man defenders to lock down their WRs, and that's not something I'm willing to gamble on. 3x2 sets are also very common so it's a dilemma you'll be dealing with all game if you run them consistently.
What's worse is the offense can manipulate your D by causing the match to trigger where you don't want it to. Even something as simple as an automotion which changes the balance of a formation can completely wreck your D, and you won't have time to adjust.
Quarter flats are bad for the same reasons, and they convert to more potential assignments (they can play curl flat, hard flat, or match man based on the offense) so they an an element of unpredictability that makes them tough to scheme around.