Tax at source lower than tax return?

Hi, I have a B permit and have been taxed at source for the whole year. However, I am doing the tax return because of deductions (e.g., 3a account).

Considered all the deductions, I end up having higher due taxes (cantonal + federal) than the withholding tax in my salary certificate, how is that possible? 

Is the federal tax included in the tax at source?

I lived for 3 months in Zug at the beginning of the year, but still if I subtract the withholding tax savings I had in those 3 months I should have a lower taxation in the end.

Thanks for your help!

It's like this:

• The tax at source is a "flat tax" so to speak, which is calculated based on averages. Depending on your income bracket, this can work in your favor, because you are taxed at the lower "average tax rate." The reason that simplified, flat withholding tax rates are used is to make it easy for employers, who are responsible for deducting this tax.
• When you submit tax returns, then you pay taxes at the actual rate that really applies to people with your income. Basically, the privilege you enjoy because of the "averages-based" withholding tax system disappears, and you pay taxes at the same rate as Swiss people.

Here's a very simplified hypothetical example:

Let's say you earn 100K per year, and your canton has a withholding tax of 5% for incomes between 80K and 120K. So your withholding tax is 5K.

Now let's say the tax rate for people who submit tax returns totals 10% for incomes in the 95k-100k tax bracket. So your standard tax if you choose to submit tax returns would be 10K, which is 5K more than you would pay if you just stuck with withholding tax.

So even if you save, say, 2K by claiming pillar 3a deductions, you would still pay 3K more in taxes.

That is why it is so important to carefully study both the witholding tax rates/brackets and the standard tax rates/brackets before you choose to submit tax returns. In many cases, you are better off just sticking with witholding tax, but there are many different factors involved (i.e. where you live, your income, your wealth, etc.). Consulting a good independent tax expert who focuses on your canton of residence could pay off over the long term.