Yes -- once, last year (i.e. 2017, when OP posted this question). It was flat-out unnerving.
I was visiting from San Francisco (to spend time with my best friend, who has since passed away), and I'd made a whole list of things I'd neglected to bring with me. Which is kind of annoying, I guess, but yeah, I showed up with a shopping list. Actually...! It was all the stuff I'd attempted to place a same-day delivery at my Airbnb for (!!!!), but for some reason the app wasn't working out, so I went to the store with my order printed out. So... everything I'd "ordered" was also in-store, I knew for a fact, because the app lets you pick from store inventory.
The employee who greeted me just said "no" to most of the things I was shopping for. I must've been visibly unnerved, and eventually -- when the employee finally left to look for a thing -- someone else approached to help. She was actually the store manager, in retrospect. She zipped with me through the store and helped me find literally everything I'd felt I needed. I was extremely grateful.
So... it was ultimately a positive experience, but at the beginning it was not.
I should probably explain... I carry a lot of extra abdominal weight due to diagnosed hypercortisolism, and I remember just assuming that this physical trait probably kept me from looking like I could afford the stuff I was asking for (it was the Sephora on Michigan Avenue, and downtown stores can be really tough on chunky people). Maybe not, and probably the employee was just having a rough afternoon -- I've worked in retail, in Chicago, for a friend, the one who just passed away actually -- but I left that Sephora feeling like that must surely be the reason I initially wasn't helped. It's just a thing I often anxiously assume, since, if you used to weigh 100 pounds and now you're quite fat, you can't help but search your environment for reasons you're treated differently now, versus then.
I've also had amazingly positive experiences at Sephora (as opposed to Ulta, where almost every experience is "someone already dug their finger into this thing I was gonna buy"), and I'm glad and thankful that I ultimately had a good experience on top of my bad experience. (The store manager rescued me from a negative employee, and she also hit the floor quite hard for me -- I will always be grateful.) So it was a real emotional rollercoaster, and I actually left with strongly mixed feelings. "Am I too disgusting to help? Was I finally helped because I matched my expensive shoes to my expensive bag?" Etc. It's a miserable death-spiral of second-guessing.
Makeup is all about finding a way to try to be comfortable with the skin we have to live in, and being mistreated in a store full of makeup is a heartbreaking experience.
Before a Sephora employee can find my post and start apologizing for my experience, I just want to point out that I will never know with real certainty why my greeter-employee was so nasty, and also that I understand that it's impossible to screen employees for anti-fat bias. Fatphobia is generally considered socially acceptable, but also, I think most people wouldn't even know they're doing it, so there's no "questionnaire" you could ever offer. So... I'm cool with it. I have to be. It's just a thing, you know?
But I wish to God the world weren't the way it is.