I think the problem is given in the error message, although it is not very easy to spot:
IndexError: too many indices for array xs = data[:, col["l1" ]]
‘Too many indices’ means you’ve given too many index values. You’ve given 2 values as you’re expecting data to be a 2D array. Numpy is complaining because data is not 2D (it’s either 1D or None).
This is a bit of a guess – I wonder if one of the filenames you pass to loadfile() points to an empty file, or a badly formatted one? If so, you might get an array returned that is either 1D, or even empty (np.array(None) does not throw an Error, so you would never know…). If you want to guard against this failure, you can insert some error checking into your loadfile function.
I highly recommend in your for loop inserting:
print(data)
This will work in Python 2.x or 3.x and might reveal the source of the issue. You might well find it is only one value of your outputs_l1 list (i.e. one file) that is giving the issue.