Unfortunately, prepositions and articles are both very hard to reason out. For those examples I would recommend "There is a typo in line 6" and "There is a typo on page 3." (If you use "on" with "line," it sounds like there is a blank line, as in a form to fill out: someone might say "Please write your full name on line 2 and your address on line 3." But if you're describing words in a line of written text, you want the preposition in.)
You can use "the" for these examples if you are using an ordinal number: "There is a typo in the 6th line" or "on the 3rd page." But you would not say "on the line 6" or "on the page 3."
And you can mix and match! "There is a typo in line 6 on the 3rd page of this paper."
I hope this helps,