There has been much debate in the past about the potential dangers of bisphenol-A leaching from polycarbonate bottles. A lot of research has been done and the European Food Standards Authority has indicated that there is no evidence of any danger from the use of polycarbonate bottles in the bottled water industry.
However, some countries have advised against the use of polycarbonate bottles in baby feeders where high sterilisation temperatures are often used. As the debate and research go on, new bottles have appeared on the market in 19L, 11L and other smaller refillable bottles with the statement "bisphenol-A free".
To my knowledge, polycarbonate cannot be made without the use of bisphenol-A, so the new bottles are not made from polycarbonate but rather PET with special additives. The additives are designed, among other things, to improve high temperature stability while maintaining the clarity of the bottle. This enables high-temperature washing without shrinkage.
However, the chemistry of the additives is fairly complex and more long-term work would be needed to ensure that recyclability is not compromised when re-worked with standard PET or that leaching of undesirable components is no longer an issue. I am sure that much work has been done already, but it may take some more years' of research before we can dispel completely all fears about unwanted chemicals entering the food chain.