Aaron Hernandez ended up being referenced at least a couple different times during Tom Brady's roast -- and not in a flattering way either ... which is why his ex-fiancée is pissed.

The late Patriots star's partner Shayanna Jenkins -- who's also the mother of his only child -- tells TMZ she's disappointed in the fact that her deceased fiancé was the butt of multiple jokes during the Netflix program ... which ended up making light of his sad story.

She says, "It’s sad that I’m trying to raise my children in such a cruel world."

Shayanna goes on to say that while Aaron is gone and many people have opinions about him and his life -- their daughter together, who's 11 years old now, is still quite present.

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She also says the fact her daughter is coming of age now as a preteen means there's no doubt she'll see what was said about her father Sunday ... coming from a bunch of grown men finding amusement in his tragic death and from someone she viewed as her hero.

Bottom line ... Shayanna thinks Aaron should've been off-limits, and he definitely wasn't.

If you didn't catch it ... Aaron was touched on -- directly and indirectly -- a number of times throughout the roast, including by Tom himself. Nikki Glaser made a joke about Aaron and a ring around his neck ... while his ex-teammate Julian Edelman made a hanging quip as well.

There were a lot of oohs and ahhs during these awkward moments ... but also, laughs.

As you all know ... Aaron took his own life in prison -- after being convicted of murder.

Obviously, an ugly period for the Pats -- but clearly, it wasn't over the line for Brady and co. ... 'cause they went there and then some. Nikki went on Howard Stern's show Monday to dissect the whole roast ... including what actually was a no-no in terms of material.

As it turns out ... the hot-button issue was his kids -- so, there weren't jokes about them. However, we're told the whole no-kids thing was a mutual understanding among the performers ... not necessarily a rule Tom himself imposed. Either way, AH was fair game.

The jokes came and went -- but it sounds like the cheap shots hurt Aaron's loved ones. Hard to tell if anyone's gonna apologize or not ... based on their vibe last night, probably not.