Hi Demifan,
Have you been able to identify which songs are being skipped on your iPod shuffle?
When I see the title of this article I think of songs that skip internally, i.e. skipping around inside the song, but it also applies to songs that are skipped.
Troubleshooting songs that skip - Apple Support
Specifically, if you can identify which songs don't get played see if you can recreate them.
Make sure song files are not damaged
If a specific song skips when you play it, it may be damaged.
1. Delete the song and update your iPod.
2. Insert the CD you used to import the song and import it again. If the CD is scratched or dirty, iTunes may not be able to import the song. Try cleaning the CD or use a different one. If the song was imported or created using a third-party application, try the following:
1. Use iTunes to import the content directly from the CD.
2. Convert the content to an iPod-compatible format using iTunes.
3. Update your iPod with the new copy of the song.
You may also want to read the rest of that article for other suggestions.
Take care,
Nubz