As for your first question, I have been unable to create a situation where there is more than one partner and nobody is preferred. The first "couple" entered is preferred. After subsequent partners are added, one cannot "uncheck" the preferred box - but has to check one of the other partners as preferred.
I don't believe you can have that situation. The checkbox at the Person > Relationships View screen is very faint. Maybe you're not seeing it on your monitor??
At any rate, I strongly suggest only BLOOD parents be given the Preferred status, if one has more than one parent. Otherwise, you can end up with non-blood ancestors in a person's ancestor report or chart.
As for your second question, it looks like you are learning what I learned after using FTM for awhile - that designating people as step-children in FTM can lead to undesirable, and unintended, consequences.
I strongly suggest not to add more than one parent as a parent for a child - and certainly not to designate them as a step-child.
I'm not familiar with the report you are referring to, but the repurcussions in other reports can be: Step-children being listed twice in a descendant chart or report - once under the blood couple and once under the one blood parent and one step-parent, step-children being included as blood descendants in a descendant chart or report of a step-ancestor, etc.
I'm wondering about your use of the word "remove" the extra parent. If you mean to "detach" the non-blood parent, fine; but I wouldn't "delete" the person from my database, if that is what you mean.
At any rate, to answer your second question, I don't know of a filter or other means to isolate on these people. Maybe the kinship report might give you some leads where you need to detach extra parents from a child.