If you have orphan places, have you every checked your sources?
One of the biggest dangers of merging data from other trees is the unrelated sources and places that are added to your database. I have literally spent days removing unrelated places and sources from my database. While I have nearly got my places under control, my sources are a disaster. I don't know how many I have for genealogical sites that no longer exist. Since I was unaware these sites ever existed, the only way they could be in my database was from merging data.
I will never again merge data either from online trees, or from gedcom files from friends again. If they have information that I want I will create the necessary people places and sources in my database.
Even if you reference a strong site like Ancestry there is nothing that will prevent it from going the way of the Brøderbund Software's genealogy site from the 1990.
I will bet you never heard of it. Well I picked up hundreds and still have several dozen references to it from merges. Interestingly, after clearing these out these references for about 7 years, I met the lady who provide my family's information to Brøderbund Software. At the time they were set up their online genealogy site to promote their new genealogy software.