From what I've read, it is because the distribution is being re-routed from pipelines to trucks. Obviously, pipelines are far more efficient which is why they were built in the first place.
Also, just my own speculation, since stealing fuel doesn't accomplish much unless you can then sell the fuel, maybe there were a lot of stations getting some or all of their supply from illegal sources and now those sources are not available?
Here's an explanation.
EXPLAINER-Mexico's fuel woes rooted in chronic theft, troubled refineries
My speculation would seem to be supported by this line.
"Fuel stolen from Pemex’s infrastructure mostly ends in the hands of the same retailers that legally sell Pemex gasoline and diesel."