"mapper_parsing_exception", "reason"=>"object mapping for [file] tried to parse field [file] as object, but found a concrete value"}
That is saying that the event has a [file] field that is a string (or number, or date, or whatever)
"file"=>"InitMDCRequestFilter.java"
but elasticsearch expects it to be an object with fields nested inside it. A field on a document cannot be a string on some documents and an object on others.
You will have to modify the event to match what elasticsearch expects. That might be as simple as
mutate { rename => { "[file]" => "[file][name]" } }
or if on some events it is a string and on others an object you might need a conditional test
if ! [file][name] { ... }
or even use ruby to test if event.get("file").is_a? String