This is a data entry error on your end ... you had to enter in only your portion of the cost basis and not the total cost basis .... the % deduction was only for the expenses.  To make the correction you need to amend both returns. 

If you only have 50% ownership in the property, then you should only be entering 50% of the cost basis for all listed assets. When it comes to less than 100% ownership on rental property, the program can only do so much. It does not, can not and will not split everything.

In situations like yours it's generally easier and simpler to report all the rental income/expenses and stuff on a separate 1065 partnership return. Then each partner's share of *everything* will be indicated on their individual K-1's. Makes things so much simpler in the end. Espeically when the property is sold or there is a change or addition to the assets/depreciation section.