due to underground streams in the area
If this is the case then the pool guy would have seen it or known about it before
the repairs were done. The "cave-ins" would have been apparent after having removed the old liner and this issue would surely have been discussed with you.
In areas of unstable ground a concrete pool base with rebar can easily be poured before installing a new liner. With your current situation, the liner will not last very long as it wears out on the edges of the indentations. The hollows will also become a haven for dirt and algae and will be hard to clean/ maintain.
You really need to get this solved now.