Depending on the program and its setup, there may be lead activity that is not being associated with the Marketo program.
For example, imagine there's a default program synced with Salesforce. In the program, there's a child asset smart campaign sending emails, and you aren't seeing this email activity in the SFDC campaign. The child asset smart campaign needs to have a Flow Step: Change Program Status [for the specific program]. (It is recommended that this is flow step #1). Even though the smart campaign is a child asset of the program, these 2 assets are still independent of each other, so the flow step is needed to sync the activity.