I know nothing about the language being discussed here, but the answer is no, it doesn't lead to misunderstandings. How do I know this? Because it's a natural language. The language exists for no reason other than the fact that it works. If the words sounded exactly the same you could safely assume that they either communicate the difference some other way, or the difference simply does not matter to them.
An example of communicating something in a different way would be how in Spanish the pronoun is completely dropped in most cases. This is because it's completely redundant as the verb will be conjugated to include the pronoun.
An example of things not mattering is in English where we don't distinguish between rivers that flow into other rivers and rivers that flow into the sea. French speakers might be confused (how do you know whether it's a fleuve or a rivière?), but the answer is we simply don't care.
When learning a natural language, always assume that it works for them. Your aim is not to be able to translate your language to theirs, it is to be able to communicate your thoughts into their minds. Keep an open mind about what's important to transfer and how this can happen.
> but the answer is no, it doesn't lead to misunderstandings
Natural languages offer misunderstandings between native speakers all the time. A sentence like "Bajó" in Spanish or "They went downstairs" in English can have many different antecedents for the listener to choose between (bad subtitle translations can give you a master class in this). If I say "the food is hot," do I mean it's temperature-hot or spicy-hot?
I would refine your statement to simply point out that natural languages aren't damned by misunderstandings because:
(1) You have the tools to disambiguate ahead of time if you think it might be ambiguous. "Maria bajó", "Maria went downstairs", "They both went downstairs together".
(2) The listener can simply ask for clarification.
(3) It doesn't necessarily matter. The point of the story was that John couldn't enjoy the soup, not whether it was too hot or too spicy.
All that said, I think the person above was just asking how similar the pronunciation was between two words.
In Korean, the vowels ㅣ (ee sound) and ㅐ (eh sound) are different in the written language. There are actually more difficult things such as ㅐ and ㅔ (both "eh" sound) which can get confusing when trying to spell Korean words. In practice, I personally don't get confused differentiating between "nee-gah" and "ne-gah", but that may have been due to me having Korean parents and being used to that terminology since birth.
An example of communicating something in a different way would be how in Spanish the pronoun is completely dropped in most cases. This is because it's completely redundant as the verb will be conjugated to include the pronoun.
An example of things not mattering is in English where we don't distinguish between rivers that flow into other rivers and rivers that flow into the sea. French speakers might be confused (how do you know whether it's a fleuve or a rivière?), but the answer is we simply don't care.
When learning a natural language, always assume that it works for them. Your aim is not to be able to translate your language to theirs, it is to be able to communicate your thoughts into their minds. Keep an open mind about what's important to transfer and how this can happen.