Once you get the Magic Bottle, you can fast-forward time by going to an alternate dimension.
You may have noticed these black holes all over the place. (I was initially confused about them, too.)
You can scoop these up with your bottle, then release them to open a portal to said dimension. It serves 2 purposes:
Fast travel. You can walk across the ocean ...
If I recall correctly from my playthrough, there is no way to do so. That really frustrated me too. Have a website ready to alt-tab to; StackOverflow is one excellent candidate.
Don't give up on it entirely because of this. There's not too many time-sensitive events, and except for a few annoying glitches and design flaws, the game plays very well.
This post on the developer's forums has hints for stuck players. It suggests those objects do indeed have significance, and that in order to interact with them you need to use an item you can collect in the game.
The post contains more information, but may also contain spoilers. Read at your own risk.
Edit: In case you don't mind spoilers. ;) These things ...
So I found out a way.
after you throw bomb on bot, he awkward rises his leg. I had this for weird animation or glitch, but it is what is supposed to happen and you have to crawl underneath it and then proceed to miner cart and shoot its cannon on bot.