Yeah, It could be the MP3 encoding. As I'm sure you know, MP3 is lossy compression. The wave shapes change and some peaks are boosted while others are reduced. I believe this "effect" is worse when the file has been (dynamically) compressed and limited.
You can also get clipping from resampling, due to "inter sample peaks".
Note that the file is not actually clipped... It goes over 0dB! It will only be clipped if you convert it to WAV or send it full-volume into your DAC (which is hard-limited to 0dB.)
Try 32-bit floating-point WAV. If that file doesn't go over 0dB, your limiter is working fine.
(16-bit and 24-bit WAV are integer formats and they absolutely cannot go over 0dB. So you won't know if the file is clipped at 0dB, or if your limiter is keeping it to 0dB.)