Run this to get a bundle containing dirt:

/give @s minecraft:bundle[minecraft:bundle_contents=[{id:"minecraft:dirt"}]]

Hold the bundle in your main hand, and enter this to check if the bundle contains a diamond:

/execute if items entity @s weapon.mainhand *[minecraft:bundle_contents~{items:{contains:[{item:"minecraft:diamond"}]}}]

Clearly, the bundle did not contain a diamond, and yet this outputs "Test passed, count: 1".

I tested this on minecraft:bundle_contents and minecraft:container. The only case I could find where this bug doesn't apply is when the collection being matched is empty.