It's okay to include the expense in both countries in order to properly account for the net income correctly.  The accounting may not work out exactly the same in both cases, as each country may not allow for the same deductions for tax purposes, but you should enter the same items on your U.S. tax return that you would as if the property were located in the U.S.. The primary thing that will be different is that the building will depreciate on a different schedule.   

When you are reporting the income to the U.S. you want to also be sure that you add any tax paid to Germany on the same income in the section Foreign Taxes Paid.