Looking into this, I see older similar issues:
Audio Crossfades Not Exporting Correctly
Audio Crossfade Issue on Tracks With Audio Effects
Both are listed as 'solved', but that seems a stretch to me.
Oct 2024, still bumping into similar issues, using v 24.5.0 (build57)
Using track effects here, solo'd the track I'm having issues with.

I shortened / combined SFX of a bowling ball rolling to hit pins. the yellow line indicates where the ball hits the pins. My outputs seemed to offset the crossfade down the timeline, removing the impact sound that I cued.

In order to get the desired effect I had to remove the crossfade entirely

Attached are two MP3s.
In addition, I was only able to repoduce the error when outputing the entire 30 sec spot - when I made a in/out range the error was not output...
I've had a similar issue in the past, but did not bother reporting it...
I know Premiere is a very complex piece of software- but if they dont want us using track based audio effects (best-practice audio mixing methodology), why do we have access to them?
The issue I'm having is not a result of a 'sh**load' of effects, and its not an artifact of audio compression (the reference I provide without the crossfade proves that).
I've rendered audio within Premiere and the problem is not present.
I've output via Media Encoder- which again, if we should't use it, why do we have access to it?
Cheers,
David
Processor Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz 4.20 GHz
Installed RAM 64.0 GB
NVIDIA GeForce RTX 4070 Ti
System type 64-bit operating system, x64-based processor
Edition Windows 10 Enterprise
Version 22H2
OS build 19045.3208
Experience Windows Feature Experience Pack 1000.19041.1000.0