I confirm i don't have this issue, i just finished the game on my raspberry pi 3, what i recommend :
- Make sure you are using fbalpha-libretro, not fbalpha2012-libretro
- Make sure you are using an updated romset (current one is 0.2.97.39)
- Make sure you are not using some exotic audio/video driver in retroarch (never had issue using gl+alsa for the past few years)
Also, you didn't mention it, what's your raspberry pi ? Raspberry pi zero and Raspberry pi 1 lack the power to run properly most games fbalpha-libretro has to offer.
If you are using a raspberry pi 3, use a 2500mA power supply, or your cpu will sometimes lower its clock, resulting in various issues.
2000mA power supply should be enough for a raspberry pi 2.
If you need more help, i recommend you ask on retropie's forum, i have my own setup on my raspberry pi, which is not based on retropie, so i'm not an expert with retropie.