Okay i will go straight. Do you miss some baseball and you already reach the end of the game? Feel lazy to start a new game and grinding again? Don't worry me too.

Usually if you miss some baseball it means yoy have around 37-40 in your bag. Total dungeon on Superdimension is 37 (Grand Library not counted because no baseball there), so logically you will get 37 ball minus 1 on Mascarasco troll ruin depth at Megadrive era. Actually there's 41 baseball you can get in your 1st playthrough (except in Mascarasco Troll Ruin Depth Megadrive era which you ONLY can get it on 2nd playthrough. For more information read How to Defeat Delphinus guide by [C.P.U.] Nowarin).

"But there's only 37 maps that we can clear so where's the others?"

This is the explanation:

There's some dungeon that will changed if we talked to a chirper or through a plan. And did you know? The baseball is available in that dungeon both before and after it's changed and you CANNOT undo it. So how you can get that ball again?
Just complete your gameplay and start NG+. The baseball will still there.

Here the place that have missable baseball

The 1st dungeon that changed is Panique Cave at Megadrive era (the oldest era). Clear that dungeon for the 1st time and you will get a baseball and some medals. After some mission there's a chirper (spelunker if i'm not mistaken) that if you talk to him, Panique Cave will be changed. Go check that dungeon again in case you missed the baseball there. So be carefull on this dungeon because it's changed if we talked to chirper. If you already collect 2 baseball from 2 version of this dungeon, maybe you missed it in next dungeon.

2nd dungeon that have missable baseball is Toypolis dungeon. To make sure you get all of the available baseball there, when you first time visit Toypolis in Segasaturn era, go visit other era (Gamegear and Dreamcast era). There's Toypolis dungeon too but make sure they're still 1 floor. Now you have 3 baseball from that dungeon (but i'm sure you're not missed baseball at Segasaturn era since it's only have one version).
Just play the game until a quest about expanding Toypolis. Complete that quest to make Gamegear and Dreamcast era Toypolis expanded to 2 floor. Go visit both eras dungeon to get another missable baseball. Make sure to check them carefully each floor. You will get one balls on 2nd floor each era.
Continue your gameplay until last quest to expanding Toypolis showed up. Complete that quest to open 3rd Toypolis floor at Dreamcast era. Go check that dungeon to get last baseball.

In total, you can miss 5 baseball in your playthrough :
One at Panique Cave Dreamcast era before it changed
Two at 1st ver. of Toypolis Gamegear and Dreamcast era 1st floor, and
Two at 2nd ver. of Toypolis Dreamcast era 1st and 2nd floor

Once again, if you missed that baseball and already finished your 1st playthrough, just start a NG+. The missable baseball is still there.

Happy farming that little ball ^^

Thanks to Ztarman for explaining to me about missable baseball and for [C.P.U.] Nowarin for "How to Defeat Delphinus Guide"