General sealant installation: Prevent three sided adhesion. Provide sealant depth of ½ joint width; minimum depth of ¼”; maximum of ½”, by using backer rod.
What we have here is incorrect installation. It appears that no backer rod was used before shooting the caulking. This caused the caulking to be much thicker than needed. More caulking does not mean a better seal. The caulking is designed to move with the expanding and contracting components on your building. When the caulking is installed to thick it will not move as designed and can fail causing leaks. Also, you see skimming. The sealant was installed to thick and most likely failed causing a leak. The hired contractor came to fix the leak and fought to remove the thick sealant. The contractor probably gave up and skimmed the joints. To the owner it appears fixed but, all they got was a band aid that will fail again soon and in this case it did.
Please make sure the contractor you choose to re caulk your building understands how to properly install sealant.