WMC is notorious for these problems and others, which is why I don't use it. But I do read about its problems and solutions, mainly on the SiliconDust forum. So while I can't give you a solution in detail, maybe I can point you in the right direction.
You didn't mention your program source but you did say that you should get WGN so I'll assume it's Verizon FiOS. WGN is in clear QAM on FiOS channel 55.100. I don't think it's in the clear on Time Warner and of course it's not available OTA. Cable companies aren't required to include PSIP identifiers for their channels as broadcasters are, and FiOS doesn't identify WGN. WMC ignores unidentified channels so you'll have to add the information manually.
The misidentification of WNYT-HD as "this TV" is trickier. I think WMC uses an online source for some of its lineup information and that source could be wrong. Just a guess. Here are current FiOS assignments that might be pertinent:
FiOS ID Real Virtual
WNYT-HD 71.1625 13.1
WNYT 63.1605 13.4
this TV 74.1617 6.2
I think I read somewhere that WMC won't let you manually add a subchannel with more than 3 digits, although it may do so automatically if everything else is OK.
has articles on editing WMC to add missing channels.http://www.thegreenbutton.tv/forums/
is a general resource for WMC, but the only help I found for your problem was the link to Hack7MC.https://www.silicondust.com/support/channels/
shows what channels may be received in your area, both OTA and on available cable services including FiOS. Unfortunately it isn't currently being updated but it's still useful.
These and other WMC problems are discussed ad nauseum in the SiliconDust forums, but while the fault usually lies with WMC, the workarounds are sometimes specific to their HDHomeRun tuners. Since you have a Hauppauge tuner you'd have to figure out what parts of the answers you can use. Maybe Hauppauge provides similar help.