In our actual world, something that seems minor, like having 3 chromosomes (trisomy) where you're supposed to have to have 2, can be devastating. Sometimes it does cause minor problems, like people with XXY instead of XY or XX.
Sometimes it causes moderate problems, like in having 3 copies of your 21st chromosome (aka Down Syndrome). In this case, brain function is altered and nearly everyone ends up with a mild to severe intellectual impairment. It also changes the facial shape, makes the person shorter than they would have been, and often affects the heart.
If the extra chromosome is on chromosome 18 or 13, the problems are extremely severe. A few children born with an extra 18 will live, but nearly all those born with an extra 13 will die in the first year, if they make it to birth in the first place. In addition to severe/profound intellectual disability, the extra chromosome often causes things like a cleft palate, cleft lip, extra fingers or toes, a nose in the wrong spot on the face, a heart condition, or under developed lungs. Among other things.
The effects of extra chromosomes elsewhere isn't really known because pretty much no embryo/fetus survives to birth. Though it's possible a few aren't in the literature because they don't cause problems so no one bothers to test for them (contrary to what you might think, trisomy is NOT picked up by consumer DNA testing commonly used for genealogical or health purposes).
Important note: some people with chromosomal differences are what you call mosaic. This means that the extra chromosome isn't in every cell, just in some. When you test chromosomes to look for trisomy, you run multiple tests so that you know if mosaicism is an issue, and so you don't miss a trisomy because you tested a regular set of cells.
Mosaicism generally causes the same problems as having the genetic difference in every cell, but it's more mild. It is also less likely to be fatal.
Absorbing a soul, by your description above, sounds like it might involve genetic transfer as well. I would think that, most of the time, it goes smoothly, but sometimes an extra chromosome will "catch" in a way that affects the host's body globally. Our bodies are really really good at fixing genetic information that goes bad (something that happens every day, in a small percentage of new cells). But sometimes we just can't fix it. That's what cancer often is; a genetic altering of our cells that our bodies can't fix.
So Elizabeth, over time, has had her genetics altered. This leads to her normal body repair mechanisms malfunctioning and rebuilding her body in ways it is not supposed to. It leads to cancerous tumors. And changes in how her brain, heart, and other organs work. All stuff that probably would kill anybody else. But she isn't able to die. She has all the soul infusions stopping that from happening. Short of cutting off her head, she's just going to continue to live, no matter how bad things get. No matter how different her body becomes.