If you have 100 mL of 50% acetic acid, that mean you have 50g of acetic acid in solution?

Nope. 50% acetic acid has density of 1.0575 g/mL, so mass of 100 mL is 105.75 g, 50% of that is acetic acid - 52.8 g.

if you have 1000mL of 5.25% acetic acid, then you have 5.25g of acetic acid in solution?

5.25% acetic acid has density of 1.0059 g/mL, mass of 1000 mL is 1005.9 g, 5.25% of that is 52.8 g.

Note that exact calculation give error of about 0.07 g, that's from the rounding errors. Probably correct concentration should be 5.24 or 5.26 - or something like that, it is almost 2 a.m. here and I am too tired to play with numbers to find out.

Where does the extra 0.25g came from???

From the assumption that solution density is constant regardless of the acetic acid concentration. It is not.

That's all caused by change in density?

Yep.

Do you mind explain concentration dependent of density? I have no clue what does that mean.

Every solution density depends on its concentration - in most cases knowing concentration you can find out (using tables) density, knowing denisty you may find out concentration.

For some substances it is not that easy. Acetic acidy density vs concentration curve has maximum at about 78%, and for example 60% and 92% solutions have the same density - knowing concentration you can find out density in tables, but knowing density you can't tell whether you have 60% or 92% solution.