The episodes are listed in their originalm broadcast order on Nickelodeon.

If you want them in another order, you need to create an episode group or use an existing one.

It has nothing to do with broadcast order. Because each individual short has been listed as a separate episode, there are multiple missing from this listing.

None are missing. They are listed based on their original broadcast dates.

I recently purchased a box set of the first six seasons. According to the box for season two, the correct order should be:

1. Your Shoe's Untied
2. Squid's Day Off
3. Something Smells
4. Bossy Boots
5. Big Pink Loser
6. Bubble Buddy
7. Dying For Pie
8. Imitation Krabs
9. Wormy 10.Patty Hype
10. Grandma's Kisses
11. Squidville
12. Pre-Hibernation Week
13. Life of Crime
14. Christmas Who? -- END DISC 1 --
15. Survival of the Idiots
16. Dumped
17. No Free Rides
18. I'm Your Biggest Fanatic
19. Mermaidman and Barnacleboy III
20. Squirrel Jokes
21. Pressure
22. The Smoking Peanut
23. Shanghaied
24. Gary Takes a Bath
25. Welcome to the Chum Bucket
26. Frankendoodle
27. The Secret Box
28. Band Geeks -- END DISC 2 --
29. The Graveyard Shift
30. Krusty Love
31. Procrastination
32. I'm With Stupid
33. Sailor Mouth
34. Artist Unknown
35. Jellyfish Hunter
36. The Fry Cook Games
37. Sandy, SpongeBob & The Worm
38. Squid on Strike

@jojo2357 said:

I recently purchased a box set of the first six seasons. According to the box for season two, the correct order should be:

As explained in our rules, we are not going as per the current DVD or Blu-Ray releases, but as per the original broadcast.

You can use an existing episode group or create a new one for your specific order.