The Michigans
Sanford School of Medicine and Stanford School of Medicine.
BC and BU
Re: 73 or so
It’s funny you mention the Grinnell/Cornell U confusion among northeasterners – there is also a school called Cornell College in Iowa.
Heck. Why do the Brits call University College London?
Hollins (people either misunderstood me to say “Rollins” or “Holland”)
Rowan University. This makes me think about Rwanda.
There are also a number of people who for some reason think USoCal is a state school–perhaps a directional. 
Cornell NY
Cornell IA
Sewanee also misspelled Suwannee. Sewanee: The University of the South thing is a whole other matter. They can’t even agree on their name.
Lehigh - easy to pronounce, often mistaken for a high school - Lee High.
This may be hard for many of you to imagine, but it was a long time before I realized that Berkeley or UCB was also Cal.
Santa Clara University yielded a lot of “why are you spending money to send your kid to an OOS public university?”
Boston University too!
SDSU can be:
San Diego State University or
South Dakota State University
John Hopkins
Oops - duplicate
IIT–in Illinois
or
IIT–in India
or did you actually mean
ITT tech?
I thought a local kid was going to Furman, when he was really going to Ferrum. I didn’t figure it out until I saw him wearing a T shirt with the name.
This happened a number of years ago but it has become legend in our family. First, our family has two “branches”, the Atlanta branch and the California branch. My young cousin (California branch) was visiting my brother in Atlanta several years ago and my brother had invited neighbors over for a bbq. During the cookout the following exchange occurred:
neighbor: Where will you be going to college next fall?
cousin: I’m going to Columbia!
neighbor: That’s wonderful! My husband went to USC and loved it.
To my cousin, this seemed like a non-sequitur but fortunately the conversation didn’t go any further. It wasn’t until later that he worked out that the neighbor thought ‘Columbia’ meant going to school in Columbia South Carolina at the University of South Carolina.
@Otterma was just going to say usc, but the California one or the south Carolina one.
Columbia University and Columbia College (Chicago)
Do you think they have to regularly swap misdirected snailmail, like the staff at the Slovenian and Slovakian Embassies do?
Absolutely! At the student store at Scripps College they sell a mug that says “We don’t study fish”.
(BTW - both are named for the same Scripps family)