They sure as heck did! There were extensive problems with the first few hundred M-1's. They were rushed into service without much testing in 1969-70 in a desperate effort to replace the rattletrap MP-54's that were falling apart daily. Within the first year various problems developed causing large numbers of them to be laid up for months pending modifications to their propulsion systems, and other problems.
Added to that was a labor dispute involving the LIRR car maintenance workers re: who was going to do the warranty work; LIRR workers or the manufacturer's (Budd Co.) personnel. After Governor Nelson Rockefeller finally intervened a settlement was reached and the work finally got done. By about 1973 the entire LIRR M-1 fleet was delivered and up and running.
BTW, the M-7's on LIRR have broken in much more successfully than the M-1's did, partly because LIRR tested them at length before starting them in revenue service. And they had more time to do it, as there isn't quite the replacement crisis with the M-1's now as there was with the 1920's era trains in 1970.