Soooo....they were offering you a bike at a price below MSRP.....
Highly doubt there was anything intentional or malicious about what happened with the quotes. It happens. As for being wrong about the MSRP....honest mistake I am sure....fact is he was still offering a bike for $300-$400 below MSRP. With some rough numbers....that could have basically cut his margin in half.
Steering you towards a bike outside of your budget...not something I like seeing shop owners do. Usually happens because "we have this one already in stock!"
Poo-pooing the idea of a used bike by making it sound like an impending train wreck - again....poor tactic. Often used in the industry. it was probably taught as a sales tactic at some poor sales training one year at interbike or by certain main line reps. It's a tactic that actually implies that the customer is ignorant. So ignorant in fact that they can't figure out whether a bike they want to buy will work.
All in all none of this would fall into what I would categorize as a "shady business." Granted we are all a part of the mass consumerism/internet generation and we are used to prices set in stone and shown up front and stored in computer systems for the whole world to refer to....but in fact this is still a cottage industry. When you get a quote for a bike and it's a "deal" I would always advise anyone to have the person who quoted it for you write it down on the business card for the shop with their name so that you can refer back to it at a later date. not saying this would give someone the right to scream if the price ever changed, but it would give a different shop employee or owner an opportunity to address it directly if the situation arrised.
Shops are run for the most part by well intentioned individuals who have an innate love for some aspect of this sport. Unfortunately most of these individuals have little to no experience in industries outside of the bike industry and as such apply only what they know or have learned from experience in the industry. They also don't tend to be highly qualified business people financially. You might see the actions as a shady move by some money loving shop owner who is trying to rob you blind, but honestly....there just isn't enough money in any of this to support individuals like that for very long. That extra $100 on that quote is a big number for many people....but when considering the average overhead in a shop....that nets out to about $3-$4 for the owner. As such it can sometimes be a little too easy for many in a shop to lose that frame of reference that most others are using when looking at price.