It may not be a design issue. It sounds as if you are looking directly as the table design and not through SSAS. If that is the case, the fact tables may be joined. In a proper OLAP design, each fact table represents a single level of granularity. It is possible that one fact table is the parent granularity to the other.
If you try to sum these as you describe, you will get wrong results because if there are two records in whichever table is the child, the main row will repeat twice. You will need to create a derived table on the child so that it sums all the data on whatever is the FK field to the parent table. Then join the results, which should be now down to a single line, to the parent table.
It would even be better to query an OLAP design through the OLAP tools. I know, however, that sometimes we have to do what we can with what we have.