Mistake: Building industries you do not need.
Why a mistake? Every new facility/industry built adds to upkeep cost and pollution. Constructing temples or libraries before needed gets you NO BENEFIT but you support all disadvantages. Remember that if an option is available does not mean you should use it!
Mistake: Extend housing before needed.
Why a mistake? Extending housing only increases your population limit, not the growth rate. While you think it is better to extend earlier so you benefit from more taxes, don't forget that unhappiness and squalor increase as well.
Mistake: Producing everything yourself.
Why a mistake? You might be tempted to construct different industries and produce as many goods as you can. It would seem a good strategy at the beginning but it's a flawed long term strategy. The costs and pollution will pile up and you will produce just enough for yourself, never having enough surplus to be competitive at the trading office. It is better to produce 1-2 main goods (which are using a common raw material) and perhaps 1 secondary if the need arises. Be aware that the hot product today will be useless tomorrow so do not be hasty to demolish what you have and build the hot industry.
Mistake: Trying to find the perfect strategy.
Why a mistake? Xemerys was inspired from reality and there is no such thing as perfection in the real world. There is no optimum strategy, product, civic, spell or propaganda in the game. Everything can be good in some situations and very bad in others. The perfect strategy is TEMPORARY and contextual. When things around you are changing, so should your strategy.
Mistake: Hating the red -
Why a mistake? Everyone feels uncomfortable when they know they are on loss (gold or good stocks), but you have to see far than that. Do not build new facilities or staff all your wheat/goat farms or bread/cheese factories just because you have a small loss per round. Many times that stock will be enough for weeks or even months. Also if your financials are in red, in many cases you can compensate and even get very rich just by exporting goods. Xemerys was designed with trade in mind, so having profit only from taxes should not be a priority.
Mistake: Staying too much on default civics.
Why a mistake? Once your city develops , you'll find that maintaining industries is harder. The default civics are good for starters but on the long term you will need to use more specialised civics, depending on your strategy. Note that every civic has both advantages and disadvantages so choose well. Of course, new civics have to be researched first.
Mistake: Playing as a single player game.
Why a mistake? Xemerys was designed to be a social game (not that kind of FB spam) and it's very hard to do anything without interacting with other players. Knowing your fellow rulers better will help you get better deals or know their weaknesses when war erupts. Not to mention negotiating secret deals and price fixing.
Mistake: Not reading the wiki, forums or just asking for help on the in-game chat.
Why a mistake? Besides the obvious reasons, Xemerys is quite different from other browser based strategies and it is a big mistake to assume that you play it just as you play another mainstream strategy. Some things will seem identical to what you know, but they are not. However, using your real life common sense you will find Xemerys very intuitive. But do not be afraid to ask questions, usually players are helpful and you might learn a trick or two.