Is there a minimum app price at app stores? Is there a limit on minimum app price? I ask as I never saw any app less than .99 in any app store (apart from free apps). Can an app be like .49 for example in Google or Amazon app store?
Yes, for non-free apps there is a minimum price for each supported currency.

As I noticed this morning when adjusting the price of one of my apps, these minimum prices are not exactly equivalent across currencies (and even if they were, they would drift over time due to exchange rate fluctuations).

For example, I set the new price of my app at $0.99 for the US and the roughly equivalent price of £0.59 for the UK.  However, I could not set such low prices for Scandinavian countries or Japan because the minimums were higher (the Japanese minimum is 99 yen, which is roughly £0.71 / US$1.16 at today's rates).

Here is the full list of minimum and maximum prices per country.

At current rates it seems that the cheapest possible non-free app would cost €0.50 (approximately US$0.72).