Sounds like the problems the BNSF was having in the Valley about 15-20 years ago with trains failing to shunt the track circuits and getting "lost" to both the CTC and the grade crossign circuits. It turned out to be overnight oxidation to the rail head creating a half-wave rectifier effect that the track circuit voltage failed to penetrate and "drop the track relays". BARTD had similar problems when it opened the line between Oakland and Concord. In BARTD's case, the oxidation was caused by overnight fog, but in the Santa Fe's case, it turned out to be chemicals from overspraying during nighttime crop spraying. The Santa Fe was trying to blame Amtrak's "rather lightweight" locomotives, even though many of them were the same model the Santa Fe was running. The Amtrak trains were usually the first ones through the affected area, but then one day, the Santa Fe lost one of its own locals . . .

If those crossing gates are tied into the PTC (they probably are because everything has to be stage managed by PTC these days), well, look at the problems Denver has been having.

Really short trains, like those Budd cars someone else mentioned, are notorious for shunting failures.