If you can tell there’s a soft spot on your roof, this most likely means that the substrate below the roofing material is damaged and deteriorating. This can be a result of the plywood sheeting becoming wet from rain above or from moisture not being able to escape from below and leading to mold/mildew growth on the wood. If there is inadequate ventilation, the probability of moisture buildup and then mold/mildew growth is much higher. This can result in rotting substrates and cause your spongy soft spots on the roof.
When we roof a house, we use a plywood substrate rather than particle board — it’s stronger and more resilient to such occurrences, so keep this in mind when making decisions on your own roof.
This photograph shows the process of replacing the substrate and installing proper ventilation (added holes, or bird block vents, in the beams to let the air pass through). You can see the rotted particle board & insulation in the top left photos, Miguel drilling holes for ventilation, properly battened insulation (cardboard material to keep insulation from blocking airflow) and then your finished product in the bottom right.