I allow bottles in the facility under the following conditions:
1. The bottles contain only water or black coffee (we make coffee in our facility so it felt silly to ban it).
2. The bottles have spill-proof lids (can tip over without spilling, screw tops or other).
3. Bottles are not stored in/above product contact areas.
4. Employees wash hands as necessary to prevent cross-contamination.
5. Bottles are kept in a sanitary condition.
6. Spills from bottles are treated as a food safety hazard and QA is involved in the response.
We have a 90 degree plant in the summer, water availability is a safety concern and if the bottles can be stored safely it's reasonable. This would be much harder for a different product line than mine however and it will be situation specific.