I think you're seeing a bug in the display part of the program. Family Echo definitely shows a dashed line between the biological parent and the biological parent's spouse, but it still shows the partnerships correctly when you examine the individuals.
This is easy to reproduce, so I don't think there is anything you can do about it, apart from bringing it to the attention of the developer.
I don't know what is considered standard practice in geneology, but family trees are typically used to show the biological and legal relationships that form a family. Stepparents are not biological or legal relationships (although they can be important relationships), so maybe the generational lines of connection should just come from the biological parents in this case. You will also run into the technical limitation in Family Echo of only being able to add two sets of parents of any type.