When the leads merge automatically, is it after they completed some action? For example, filling out a form? If a form is submitted and the email address field is not included, Marketo may be merging records based on tracking information alone.
For example, say I have an event registration page and do not ask for email address. Then, one person from the company registers 6 different people. Marketo would merge those 6 people into one lead because the form was completed from the same computer and there was no email address to differentiate the people.
For the second issue - could this be related? Perhaps lead A was scored and lead B was scored then they were merged to create lead C. Now lead C would appear to have been scored twice.
If you attached an activity history of a lead that is exhibiting one of these issues, it would help. And, of course, Marketo support is always great to reach out to.