There's a few things that may be preventing you from getting Lily pregnant:
1. She has to be at love level 4
2. She might be pregnant already (it takes a few days to show, and then a few more to give birth)
3. You might already have a kid with Lily in the daycare
4. You might not have visited the Nexus yet
As for the college, just continue Veronica and Madison's storylines until they're at love level 4 and then talk to Madison in her Mansion.