The main thing I dislike about eBay search is all the sponsored placements violating the sorting order. For example, if you sort on increasing price, sponsored placements not in the specified sorting order litter that heavily, making it hard to follow. Amazon searches have the same problem. (Problem, from the perspective of buyer-on-the-marketplace.)
The other thing I dislike about both eBay and Amazon searches is the spamming of huge numbers of listings for essentially the same item. I notice it more on Amazon than eBay.
The worst thing is when you are searching for an item, but most of the listings are those "multiple different specification" listings. e.g. a seller has 8GB, 16GB and 32GB USB sticks. It's almost impossible to compare listings and the price you see is clickbait because once you click through you find the thing you were searching for is several times higher. I wrote a bookmarklet to remove all these, but that's not ideal because it can over-correct.
I wonder whether I see it less often because my bookmarked search queries are careful to avoid things in the URL that look like they might be IDs for cached queries/results.
Also, a few times I wondered whether I was accidentally triggering anti-scraping poisoning measures, even though I was doing the search and paging manually.