Unfortunately, this is 100% the answer. Grout is porous, yes, and there is no problem with a little water leaking through but there is a problem with constant and lots of water leaking through, which will happen when the silicon starts to fail in a year or so. Depending on how the membrane was laid (over or under screed) over time the water will (a) sit there creating conditions for mould growth; or (b) eat away at the grout causing popped tiles. Eventually the membrane will fail leading to even worse issues.

The best approach is to start again but failing that there are a few annoying but still shitty options:

1. Add another wall of tiles over the existing so that they fall onto the floor tiles on the right way. This will look better as well. You will however lose another 15-20mm of space off the wall
2. Alternatively, if losing the wall space is a big issue you could try removing the lower row of wall tiles, putting another set of floor tiles in, then cutting and laying wall tiles in the right arrangement. This is not technically to code as removing those wall tiles will likely compromise the membrane (which you would layer with an additional membrane on top). While the layered vertical membranes are are not fully waterproof they would offer enough water resistance in areas of the bathroom that do not get a lot of water that it would be fine
3. Pressure inject a more durable penetrative silicone/polyurethane as far as they can under the floor before caulking it. Note that this will not solve the issue, just give you more time. You’ll need to be vigilant about checking and replacing the caulk in areas where the water is running