You can definately use multiple data sources within a workbook. I would double check you haven't accidentally dragged a field from the second datasource onto the worksheet. You can tell if a field is from a linked source because there will be a little icon next to the name on your worksheet.
A screen shot of your two worksheets would help determine your issue!
+1 on Nathan's answer. When viewing each of the sheets in your dashboards, do any of them show both data sources with check marks on them (one blue, and one orange)? If so, you've inadvertently implemented the Data Blending feature of Tableau - a very cool feature, but not one it sounds like you need!
IF you see that both data sources are in play (both have check marks), look at al the shelves for y our viz (Rows, Columns, Line of Detail, etc.) and look for pills with orange icons superimposed them. They're likely to be your problem children.
It was the global filter that was causing the problem. It added the field that I was filtering on to every page.