I visited Madrid in September and found that a two or three of the metro lines were closed for maintenance completely for a significant portion of the line. Apart from this the remainder of the trains worked fine.
I did find that there was a lack of information - it was not clear at the outset of a journey that the lines were closed and the new airport link was open but this was difficult to tell and judging by the low number of tourists using the link few other people knew too.
If you are going to Madrid don't assume that you will be able to travel freely without hitting problems and closures
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