That may not have been cross contamination. Not keeping his bottles clean, not flooding the lands on the cap when filling etc, are also likely causes. Alternatively, take a large mouthed container with you marked "dirty!" Fill it with filtered water. Add a puritab. Put input tube into soak. That way you are certain.

It's also worth mentioning that no filter is effective against viruses. You require a purifier for that. I use a three stage process:
1) Milbank bag to deal with most of the turbidity.
2) Filter.
3) Puritab. Contact time according to temperature.
4) Neutralising tab when I want to drink it.

All that assumes that I cannot boil the water.