Consider the following examples:
1) In the experimental group, we observed that 65.7% of samples were infected, while the infection rate in the control group was much lower (42.4%).
2) The virus spread more quickly in the control group than the experimental group, providing evidence that the treatment was effective at slowing the infection rate.
In these two examples, the term "infection rate" is used with two completely different meanings: the first example uses "infection rate" to mean "percentage of samples infected", while the same phrase in the second sentence refers to a change in infection over time.
The problem here is that the word "rate" in everyday English is nearly synonymous with "percentage", giving us sentences such as:
"She has a very high success rate with these kinds of projects." = "She successfully completes a large percentage of these projects."
"The seat belt usage rate is up 3%." = "The percentage of passengers using seat belts increased 3%."
It's not wrong, but it's imprecise. Scientifically speaking, "percentage" means "part of a whole" and "rate" means "change over time". In documents where precision is key, such as academic papers, making your readers guess whether you intend "rate" in its common usage or in its scientific usage is, at best, a bit lazy and, at worst, can lead to a complete misunderstanding of what you're trying to say. Yes, in your particular field the term "infection rate" might be used all over the literature to mean "percentage of samples infected", so much so that it's become accepted, standard practice. I'd still argue that it's a bit sloppy, especially when it's not difficult to write with more precision. Here's the first example rewritten:
"We observed that 65.7% of the samples in the experimental group were infected, compared with 42.4% in the control group."
I know many of you will disagree with me, but small steps towards clearer writing really can make a difference! Try using "percentage", "proportion", or "frequency" (with the last being less ideal as it also implies a connection with time, but a move in the right direction nonetheless) and see if you don't feel just a little bit more confident that you've said exactly what you meant to say.