Why does this not work?
Ne, ty stroje nejsou dobrá.
Stroj Is a masculine inanimate noun and the adjective (dobrý) has to match the ending with it. So you get masculine inanimate nominative plural ending "dobré".
"Ne, nejsou ty stroje dobré." was marked wrong. Why?
the word order is a bit odd. i added it anyway.
The sentence "Ne, ty stroje jsou nedobré" was marked incorrect.
Is it incorrect to negate "good" instead of "is"?
It's very, very unusual. Nedobrý (though such a word exists) sounds kinda Newspeak-ish, like English 'ungood.' You should negate the verb instead.
"Ne, ty mašíny nejsou dobré." Why is this wrong?
mašiny, not mašÍny Diacritics is important.
"Ne, ty mašiny nejsou dobré." is accepted.