My mother is a nonresident alien living in Europe. She receives my fathers social security pension and his army retirement since he passed away in 2003. She always filed a 1040 form, since 2003, and never had a problem since. Now the IRS is asking for a copy of her green card, which she does not have, and after calling the IRS I am worried, that we did something wrong and that she will have to pay everything back, because she wrongfully had all taxes, which were withheld, paid back. She is 70 years old and can not afford this, because this is her total income. Can anyone help?

As a nonresident, your mother must file nonresident tax return Form 1040NR. On that return, she will not get standard deduction. IRS does not care about the age.
If she is getting SS benefits, it may not be taxable. You will have to redo the tax returns.

MukatA has it right; your mother filed incorrectly, which is why the IRS asked to see her green card.

Amending the return should not be too difficult, though it may cost her some additional taxes.

Unfortunately 85% of the social security benefits will likely be taxed in the U.S. Code § 871(a)(3). The tax rate will be a flat 30% unless reduced by treaty. Code § 871(a)(1). Depending on which country she is in, she may be able to claim a reduced rate under a tax treaty. If she owes taxes in Europe, she may be able to claim the U.S. taxes paid as a credit against her local tax. This would depend on which country she resides in and this would be a question for her local tax advisor.

With regard to the pension, if she is in a treaty country, there is a good chance that she can entirely avoid U.S. tax on this amount.

Conversely to IntlTax's advice about claiming a credit on her local tax bill for U.S. taxes paid, she may be able to claim a credit for taxes paid to her host country using Form 1116.

Note that she can do one or the other, but NOT both!

Since she is a nonresident alien not engaged in a U.S. trade or business, she will not be able to claim any foreign tax credits on Form 1116. Code § 901(b)(4).