Kasic, the waves aren't random, its just every ball you miss (hits below the screen), makes you lose a life (those are the bubbles at the top that fall down). If you lose 3 lives, a wave comes and covers up what you are currently trying to beat. The counter at the top right will show how many balls are on the screen. If there are 100+ balls, you lose and have to restart (this is when you thought the game was randomly ending). I have no idea what causes the prediction lines to appear, but I'm guessing they are caused if you get a streak (a certain numbers of bubbles hitting the other bubbles in a row).
woogiescrosman3, you get more crates by either finding stock (which will only give you a limited amount), or finding and upgrading factories in the 'find factory' mission (which will give you extra stock each turn. Press + if this helps!
Whenever I click outside the screen and press the continue button, it brings me to another site. I then close the site only to find that the game continued, and my guy is dead. Is there some way to change the game so it doesn't do this?
In creative mode, if you go high enough into the sky, you will find a secret base full of cobwebs, treasure and monster spawners. It is pretty well hidden, but a good improvement.
NemirPyxl is right, if you look at Other Games by this Developer (right under the game), you will see that Upgrade Complete and Upgrade Complete 2 are not in there!
The merchant arrives after you have completed 2 runs. He will sell you (in order) an obsidian shield for 450 gold, then a pair of Emerald boots for 475 gold, Wolf Gloves for 600 gold, an Eagle's Talon (sword) for 700 gold, Pixie Pants also for 700 gold, and finally a Regeneration Ring for 1000 gold. As soon as you leave to do another run, he will get these items, but after the Regeneration Ring, he won't won't sell to you anymore. If this was useful, please click + so other people can see this!
 "Fleeing the Complex"){kind=icon}
 "Snail"){kind=icon}
 "Bubble Sky"){kind=icon}
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 "Icy Gifts"){kind=icon}
 "Decision:Medieval"){kind=icon}
 "Tower of Greed"){kind=icon}
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 "Upgrade Complete 3"){kind=icon}
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 "The Enchanted Cave 2"){kind=icon}
 "Sonny"){kind=icon}
The skyhold is how you get to the ender. :D