PIE might not actually even exist, there is no proof of it. The hypothesis is that there used to be only one language in the Indo-Europes 4500-2500 BCE, And and as speakers were mose isolated, regional dialects began to form, and thousands of years later they became distinct languages. But we don’t know anything about PIE itself. It’s a mess.

Anyways, as for your question: they noticed things off about some words, and it was theorized that there were other letters. These are the Laryngeals.