I always put my wife's name in the reservation with a note that she'll be checking in, if I'm going to be late or not there at all. Of course if website does not allow for that, then I'll call and ask for a note. Only time I had a problem was when my daughter checked in at Athens Hilton. They asked her to make sure her dad checked with the front desk when I arrived. They did offer Club Lounge access (I was Gold at the time), but they charged for wifi.

You made a tactical error having your wife check in when her name is not on the reservation. This is where the Hilton website is nice, allowing for second person name and comment field.