There can be 2 types of issues with Earthquake resistant building showing cracks-

1. Not following the safety code/standards: In Nepal its quite easy to bypass the law and regulations. What I heard from one of the radio is, most high rise in Nepal has approval from the government to follow the regulations but contractors only build with regulation in lower floors and compromise the safety in upper floors, as nobody often followup on safety check. I think that is what happened in Nepal earthquake case. As the earthquake was 7.9 at its core, its impact is even reduced while arriving at Kathmandu.

2. The nature of Earthquake - The seismic waves generated at the time of earthquake fault movement are not all of a uniform character to all buildings. As these waves pass through the earth on their way from the fault to the building site, they are modified by the soil and rock media through which they pass. In simple terms, depending on the earthquake frequency and resonance in respect to the building frequency, toughest building can collapse.

http://imaginationstationtoledo.org/content/2011/03/can-you-build-an-earthquake-proof-building/