Hi Karen and Yakamoz, I will try and explain.
Here goes:
For the purposes of this hypothetical example, I have calculated as if this is your very first Visa.
You enter Turkey on 1 April 2014 on a 90/180 day visa - valid until 27 September 2014.
On your first visit you stay 21 days.
You come in again on 28 August and stay 28 days.
No problem here you have been in Turkey for a total of 49 days prior to your date of departure.
You enter Turkey again on 1 October on a new 90/180 day visa and stay for 90 days departing on 29 December 2014.
Here is where your problem will arise. Passport control will count back 180 days from 29 December 2014 which takes you back to 3 July 2014.
You have been in Turkey for 90 days on this visit and 28 days from 28 August, a total of 118 days in the last 180. Therefore you have exceeded the 90 dayrule by 28 days.
Hope this has helped. Here is also a brilliant link from Kalkan News which I think explains things clearly
http://kalkan.turkishlocalnews.com/portal/component/content/article/67-residency-and-visas/319528-obtaining-a-visa-to-enter-turkey-as-a-visitor?directory=53