Made a hot sauce recently that has common ingredients found in many hot sauces. Habaneros, onions, garlic, carrots, lime juice, sugar, vinegar, tomato, salt and fruit. I used a mix of habeneros and Fresno peppers, noticed the fresno pepper had a lot of seeds. The sauce tastes great but has a very mild bitterness at the end. Is it possible that the seed ratio to sauce is giving it that mild bitterness? The balance between vinegars, lime juice and acids from the tomatoes are well balanced by the amount of sugar. Can't think of anything else, don't ever have this problem with peppers with a lower seeds ratio. Thank you
Both tomato and pepper seeds can be a source of off flavors, including bitterness ... but they have to be cracked open, either by crushing, grinding, pulverizing, blending, etc.
If the sauce isn't something that you can easily strain the seeds out of, such as with a food mill, and you can't just leave the seeds in whole, you can take the seeds out before processing.
Some peppers, especially dried ones can be seeded by cutting around the stem, then gently pulling the bundle of seeds out. You will then want to bang the peppers against the counter a few times, then shake them with the opening down to get rid of (most of) the seeds. This will leave most of the white membrane intact, which is where the heat is.
If you're willing to lose a bit of the membrane, you can hold the stem in your non-knife hand, hold it with the stem up, and slice down the sides of the pepper. You'll end up with slabs of pepper that can be sliced or diced without losing much of the flesh. (and it's fast .. although if you learn to start each cut with a slight curve out then back in, you'll reduce the chance of knocking off too many seeds from around the stem) Also, depending on the pepper, you might end up with the bottom on its own (or still attached by membrane to the stem)