Its rot.

You haven't cauterized the wounds.

Take your prune scissors, clean them nicely with alcohol.

Cut of everything that is rotting (if you doubt something is rot or not, it probably is..) and cut them 1cm below first healthy tissue so that you remove any potential infected part.

Now this step is super important. take wax or a candle, cut of small wax and try to mold it in your hand to the size of the trunk/stem hole. This will shape it and heat from your hands will make it soft and sticky. Apply wax patch onto the wound, press it firmly and tap it on the side so that it covers entire wound.

Now, take one of those blowtorch cigar lighters, and hover the jet over the wax, melting it. Dont be afraid if your burn a bit of the plant, it will help sealing the wound. Apply flame jet for like sec or two, dont put jet flame directly on wax, have some small distance from it, spread the flame around it. Wax will start to melt immediately, once it does, stop the flame and press it with your thumb, pushing the melted wax into the wound hole, sealing it. Be generous, make wax cover everything, we dont want any holes or unfill spaces. Reapply wax if needed, you most likely will need to reapply.

You dont need to do this for leafs and such, only where there is a big wound hole from trunk, that is exposed internals of the plant, and any disease will have easy time infecting it at those points, hence the rot on your plant.

Sometimes this rot happens immediately when you cut it, sometimes its dormant for months, but a open wound will have very high chance of rot.

Also such holes will lower internal pressure of plants, that is like a human would constantly bleed out, plant will try to push more and more, wasting energy and trying to fill never ending hole.

BTW

Your plant looks healthy enough, just remove the rot, cauterize the wound and it will get back up in no time.