Check with the warranty department and see what brand shingle was used. Most likely this is a Tamko issue. They had a bad batch of underlayment used which will turn into a liquid tar substance. Tamko will normally cover replacement but there are hoops you have to jump through. Please check out the link below from our sister company and see if this is similar to what you see. If so give us a call at 866-259-2364. We can take pictures for submission to Tamko.
TAMKO(R) Warranty Inspections | The Roof Guys