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Please explain what the problem is. As long as each object has a unique id, there shouldn't be a problem.

For debugging add a println statement in the Customer class's constructor that prints out...

You need to do some debugging to show what the code is doing.
Add lots of printlns to print out the values of the variables used it the code.
For example:
Print out the value of c inside the for...

Where? I don't see it in the post.

Can you explain when the responses are valid
and when they are invalid?
What is different from when the response is valid
and when it is invalid?

Please copy the contents of the console from...

why is this statement used?

if (trans != null) {

Where does the method create an instance of the Transaction class that it is supposed to return?

What is the problem you are trying to solve in "this situation"?
Does the findCustomer() method solve that problem for you?

Is there a need to create the newC object? Can the code use a local variable to hold the data read from the Scanner object?

The method is supposed to return a Transaction object. It should ask...