oh

That looks like a plains biome so lightning is a possibility (and I see no lightning rods or roof that would protect the cow hole).

Base on the wiki https://minecraft.wiki/w/Thunderstorm#Effects_on_mobs lightning would do 5 damage to each mob in range which might suffice to kill all of the cows if all were previously damaged the last time you slaughtered beef. [Cows have 10 health when at full health.]

Since lighting can damage mobs in a 6x12x6 volume, but only starts fires in a 2 block radius of where its strikes, there is an 'annular' area in which a lightning strike would damage the cows with out having a chance of setting the farm on fire directly – and any fire started in the 'annulus' would likely go out before spreading. (Any fire that reached the farm might also have been extiguished by the rain as well.)

Because lightning is a simpler explanation than a random glitch, I'd be inclined to think this was the cause.
[Back in the 1.12 days I lost a set of 4 blue sheep despite their being underground as lighting can damage entities starting from three blocks lower than the point of the strike.

Sine then (until the introduction of lighting rods), I became very assiduous about keeping stock pens lightning proof.]

Without lighting rods, the heads of any animals need to be greater than three blocks below the "highest block that is liquid or obstructs movement" and a minimum of seven blocks in from the edge of the roof.
For the 1x1 cow hole you've got, a roof in the thirrd block above the fence and extending six blocks from the fence in each direction (13x13 roof) would be needed to avoid direct entity damage.

Additionally, because of the potential for fire to spread under the roof, the blocks at and for at least 2 blocks in from the roof edge/dripline should be non-flamable.