Yes, these words exist in Japanese and they are often difficult to teach to learners because (at least in my experience), when shown the difference, sometimes they don't see what's different. The classic example is 箸(はし
and 橋(はし
. These are really obviously different to a native but the nuance isn't so obvious to a learner. The difference between them being the intonation, HAshi vs haSHI. Add 端(はし
to the mix which sounds like haSHI but extends its intonation to the following particle and you've got a group of confused students. There's also other examples like 黒海(こっかい
and 国会(こっかい
.
But this is a topic that you just need a bit of listening practice to get right, and even then, if you travel in Japan, you may find yourself in a situation where the assumptions for intonation are completely reversed. Fortunately, context is king and you'll eventually get used to it.