The opponent bid 'atleast 5 6s' I challenged and there were only 3 6s. It said I lost the challenge and I lost a die.

Shouldn't I have won...is this a bug or am I really confused?

it counts both yours and theirs and 1's are wild.

There were only 3 6s total but I forgot that about 1s!

edit: D'oh. There were 2 1s.

no worries. glad to help