Tile Roof:
Let me preface by saying that there are limited photos of the roof and I was not onsite, so my comments are limited to the photos taken by the inspector and should not be used to determine overall roof condition. With that said, there are several indications that the workmanship is substandard such as the following:
1. sloppy tile cuts around flashing. Zoom in behind the flue pipe.
2. too much offset of roof penetrations through sheathing access holes,
3. use of mortar at joints and hip transitions rather than terminals
Should be this to make sure that the ridge to hip transition tiles are fully fastened and sealed.
4. Too tight valley with no mortar closing/sealing off tile ends
5. Soil stack detached at roof top.
Flat Roof:
1. Simply speaking, this bubbling referred to in the inspection report is actually blistering which is an indication of overheating. My suspicion is that area of modified bitumen is not sloped properly causing "ponding" as indicated by the stains and this standing water is absorbing more heat from the sun, which in turn causes the blistering. This is typically not a sign of water intrusion; however, mod bit/roll roofing is not made to withstand ponding, especially for any length of time. Most flat roof membrane manufacturers like Carlisle and Firestone void a warranty if ponding persists past 48 hours. The things to check on a flat roof are cracking/alligatoring of the membrane, vertical and horizontal seams, roof to wall transitions and flashing, and perimeter termination, which are all points os possible water intrusion.
While these are workmanship issues that indicate quality, or lack thereof, issues, they may or may not ever actively leak. I would have a professional roofer do an inspection to check on these issues and others that I cannot see from photos. I am primarily a retail residential and commercial roofing estimator here in Dayton. However, I do prepurchase roof inspections as favors for realtor that trust me following many home inspections. I ALWAYS recommend home purchasers get individual inspections for roofing, electrical, HVAC, and plumbing in addition to a whole house inspection. This way experts in the areas that carry the greatest future expense in the event of a failure/breakdown can provide a better idea of the condition of those items, potentially identifying issues up front, subsequently helping your purchase up front and maintenance cost down the road.
Hope this helps some. Best of luck.