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Why am I getting a messy signal FFT instead of a smooth one?

Hi
I am doing wave simulation on plates with various damages. Guided sinusoidal waves are generated and scattered throughout the plate. To compare the results I am getting FFt of displacement (frequency domain). The one without damage gives me a very smooth FFT while the ones with damage give me a messy FFT ( Please see the attached photo). Is it something to do with filtering or is any thing wrong with my results ?
 
Damages model
http://oi42.tinypic.com/zo6ty9.jpg

Undamaged model
http://oi41.tinypic.com/25uid8m.jpg

analysis duration is 6e-4 second but I get better shape in damaged model when I limit the analysis time to 2e-4. could be reflections from boundary ?
Cheers

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