Harriet

Stems, every time, they cost you nothing to remove. Then use ripe red peppers or at least a mix rather than all green. Garlic and coriander stems in smaller amounts are fine; it is the quantity over three weeks that does it.

You have listed four causes in one sentence and the batch is almost certainly salvageable. Green jalapenos carry a grassy bitter edge that fermenting does not remove and sometimes emphasises. The stems definitely contribute. A whole head of garlic over three weeks turns harsh. Coriander stems go bitter on a long ferment.

So nothing has gone wrong, it is the recipe. Which is good news, because flavour is fixable and spoilage is not.