It is fact. In Texas, an individual must obtain a permit from the Texas Department of Public Safety to purchase an Erlenmeyer flask, among other equipment typically used in the production of meth and other illegal drugs that can be produced from commonly available ingredients. Many of the other pieces of equipment regulated under the same statute include the kind of equipment you saw in Breaking Bad in the original RV lab.
As an aside, if you have a Bunsen burner to heat flasks and/or to create an upward draft for your home yeast lab, that is also regulated under the same statute.
In 1987 (and amended in 1989) the state legislature passed a law regulating the purchase and acquisition of chemicals and equipment commonly used in the production of meth and other illegal drugs. Under this law, businesses and individuals who purchase identified equipment and/or chemicals must obtain a permit prior to placing an order or accepting delivery of such items. The seller must report the transaction to the Texas DPS who records the transaction in a database. The permit requires the holder to perform certain security measures to prevent theft. The permit is free to acquire so long as the applicant agrees to the security measures and authorizes the DPS to inspect the location where the equipment is used and stored. A permit lasts one year, after which a new permit must be issued before new purchases may be made.
I've seen comments from people that people who make meth do not shop/steal from homebrew shops so there's no reason for the homebrew stores to be concerned. I know personally that one of the local homebrew stores has a sign out that the Idophor is not the type of iodine used to make meth so there's no reason to steal it. I asked about it and they told me they have had some bottles of the fairly cheap sanitizer disappear out the door. Even if the premise of the comments was correct, it still isn't a good idea for stores to expose themselves to liability under the statute for keeping the Erlenmeyer flasks on the shelves. Who knows when a DPS officer might walk in, even if it's just to buy some brewing supplies.
This statute would require homebrewers acquiring Erlenmeyer flasks to first obtain permits and for homebrew shops to report any transaction to the DPS. Because the homebrew stores take delivery of the equipment from their wholesaler, they must also have a permit and store the equipment appropriately.
In all likelihood, the DPS probably isn't going to come bust down a homebrewer's door for buying an Erlenmeyer flask without a permit but with the DPS who really knows. Better to get that permit than face the long list of penalties in the Health & Safety Code. If the crackdown comes it will most likely fall on the stores, who are more of a risk of selling to the wrong people or having their inventory stolen.