There are many, many situations in the game where this happens.
This can’t be intentional.
At times it works the other way around: an 87% chance only to miss 3 hits in a row with the sniper. Other times a pixel is the difference between 87% and 14%.
I’ve seen some crazy weird angles with the heavy, only to miss the easy ones.
In that image, my guess is that the one in cover “blocks” your line of sight.
Which would be a bug, hence the title.
There is a saying amongst the XCOM community to express total exasperation toward the hit/miss percentages in the game.
“That’s XCOM baby!”
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Or it was designed that way, hence no bug.