Unfortunately, this "bubbling" or puckering of the liner generally means that the liner has stretched and is either taking on air or water behind it. The cause of the stretch in a liner that is only 3 to 4 years old, is usually due to improper chemical maintenance of the pool. Maintaining a too low ph level and not properly dosing acid bearing chemicals into a vinyl covered pool, will over a short period of time cause irreparable damage. Before I knew any better, I just simply dumped all my chemicals into the deep end of the pool as per the instructions of the pool maintenance folks. This turned out to be bad advice, because as in your situation, my liner began to pucker when it was only into it's third or fourth season of use. Not too long after that my liner was floating badly and had to be replaced.
The new vinyl liner installer advised me that acids should not be dumped directly into the pool, but rather should be highly diluted with water and slowly introduced. Because I had a rather simple equipment setup, he recommended that I introduce my granular acid bearing chemicals at the skimmer with the use of a skimmer sock, in low doses. This will minimize any potential harm to the liner when using the acids. However, this is not a preferred method if you have equipment that can be potentially harmed by the acids and would be expensive to repair/replace, such as an in line gas fired heater. Since I don't have such equipment, the worst I risk is replacing pump and valve seals that prematurely wear out. But, considering the cost of a new liner, I am willing to take that risk. I am into my sixth season with the liner, and it is as tight as the day it was installed.
If you were using stabilized pucks for sanitation, the ph of the water would have to be monitored closely since the cya, over time, will cause the ph to drop to dangerous levels without counter measures. Hopefully, you've been around long enough to already know this.
At any rate, your current situation could be somewhat ameliorated by having a liner professional work out those puckering lines by either stretching them out, or draining from behind the liner if water has accumulated there. But be forewarned, these are only temporary stop gap measures, which in my case, did not last too long.
