During a remodel of our bathroom, the workers broke the cement from around our glass block window in out shower. They told me to just fill it with thinset mortar when I tile but I am not sure about that. Is that correct information or should a use another product to fill in the holes. The current border around the window looks like cement.

Thinset does look a bit like cement, maybe you were thinking of the gluey stuff acrylic modified thinset used for floor tiles on a sub floor.

During a remodel of our bathroom, the workers broke the cement from around our glass block window in out shower. They told me to just fill it with thinset mortar when I tile but I am not sure about that. Is that correct information or should a use another product to fill in the holes. The current border around the window looks like cement.
What should I use to fill in the holes?

You should use Type S Portland for this application. It's a very high-strength mix. This was recommended when I installed a glass block window in my shower. Thinset won't have the strength to hold up over time.

Portland cement, the fundamental ingredient in concrete, is a calcium silicate cement made with a combination of calcium, silicon, aluminum, and iron. Thinset is cement with sand. Who said thinset will not hold up?

I was told this at the distributor that sold me my glass block window (long-time friends). To be clear, they said that the Type S was a better, stronger product to use for this application.

I just questioned your statement that "Thinset won't have the strength to hold up over time." Thinset is perfectly fine for patching the holes in this application. Once cured both cements are water proof and will work.