A soft shell of turtles the most time causes in missing vitamins and other substances.
The most needed substances are given with the food but some could only be given as pre-form and the turtle has to produce the useable form itself. For this the turtle need UV light (like sunlight or a special bulb at the basking area).
For more information about the UV light look at the answer here: Do aquarium turtles require basking everyday?
For the food it is important to know that pellets and other buyable dry food for turtles is more suited to the production cycle of the company than to turtles. But once a week pellets are okay. (In general is a 2 week rhythm a good idea for a healthy turtle. This means 14 times in 2 weeks (every day) another food).
Musk turtles favor non-vegan food. In nature they eat 20 percent vegetable but in the tank they very rare eat greens. Some people say their turtle eats some duckweed sometimes.
Some examples of healthy turtle food:
Dry food-animals like dry fish (for example for cats), dry prawn, dry gammarus (common freshwater shrimp), dry silkworm pupae and dry mealworms. They are a fast feed able food if you are in a hurry.
Frozen food like smelt, sunbleak topmouth gudgeon, crucian carp, bloodworms (mosquito larvae), artemia, cyclops, bosminid waterfleas, krill, mysis, cuttlefish, tubifex, daphnia, prawn, conch meat, gammerus pulex, grasshopper, mice or chicks. This is a quick solution too. Before feeding it is very important that the food is not frozen anymore. Another point to look for is this: the food should in no case be a muddy mush after thawing because then it was decayed before freezing.
Living food like snails, bloodworms, prawn, crab, water strider (and other water insects), any fish (in some countries it is not allowed to feed living fish), common freshwater shrimps, woodlouses, grasshoppers, earthworms, mealworms and cockroaches (black beetles [zool.]). Here it is a good idea to search for a clean pond in your surrounding so you catch for example insects and shrimp from it. Please think about it: in nature the turtle eats fresh food every day. In it is all the turtle needs. In frozen or dry food the sensible substances are destroyed. Fresh food is useful!
Calcium is very important for the stability of bones and shell. The most times feeding could not give enough of it. But one should not scatter chalk over the food because then the turtle could not measure the right intake of chalk (for calcium). A better idea is the cuttlebone of a sepia. This is most time offered for bird. One of it floating in the tank is enough, so the turtle could bite parts of it if needed.
A last interesting point is the so called "turtle pudding". This one could cook yourself or sometimes (rare) they are offered to buy. To cook it is only useful if you have some animals. For one alone it is to much work.
I hope I could give you an imagination what food your turtle like. And next time if you are outside you could have a jar or plastic box with you, to collect it. The turtle will be very thankful!
At last: another reason for soft shell could be toxic substances in the water. For this you should make a water test and post the result as comment under your question (maybe with "@trondhansen" in it, he is most active with water quality)
Source for the food list was the feeding part of this german website: www.zierschildkroete.de It offers pictures of the most dry, frozen and living food ("getrocknete Futtertiere", "Frostfutter", "Lebendfutter").