For example, in all the MP3s I've listened to I have heard a pre-echo only once: in a pre-echo demonstration on Wikipedia (where the pre-echo was even amplified).
Shortcomings exist, but were never relevant to the masses.
Besides, the alternative to MP3 back then wasn't using another format, it was "I cannot download music at home".
Opus 1.3: "libopus 1.3 was released on October 18, 2018" [1]
I feel like this is like asking "Why didn't Intel realize how flawed 8086 processor was, the Mac M1 makes the x86 look like a joke."
MP3 is so much older than Opus 1.3 hardly a fair comparison to expect 1991 tech to anticipate 2018's music styles, dynamic range, processing power, etc...
[0] https://en.wikipedia.org/wiki/MP3#Fraunhofer_example_impleme...
Given its age, it has held up remarkably well. You've probably simply found a particular composition that it is just not suited for. But it would have been impossible for Fraunhofer to test against all possible music compositions.