That's exactly why I read the article! I wanted to see the statement from the train company explaining how they're fixing that!

There isn’t really a way short of fixing this short of building brand new replacement tunnels at great expense.

You can’t really widen the tunnels, because the tunnel lining itself is the structure preventing water seepage, cave-in, etc.

It should also be noted that the London underground (the space underground, not the rail system) is extremely convoluted as people have been building stuff there for centuries.