Doubt while Meditating regarding Breath
The meditation taught in the old scriptures includes being aware of both long &amp; short breathing. 

Long breathing is calming &amp; soothing, which is why it feels preferable. 

Short breathing can be a sign of stored tension coming to the surface of awareness; therefore short breathing can feel uncomfortable. 

However, it is sometimes important to allow tensions to rise up so they can dissolve. This requires patience &amp; forbearance. Once tensions &amp; short breathing resolve, the breathing will naturally become long again. 

If short breathing becomes too uncomfortable, you can deliberately take some deliberate long breaths to slow down &amp; calm your body &amp; mind. 

The old scriptures state:


  There is the case where a monk...sits down...holding his body erect...setting mindfulness to the fore. Always mindful, he breathes
  in; mindful he breathes out.
  
  [1] Breathing in long, he discerns, 'I am breathing in long'; or breathing out long, he discerns, 'I am breathing out long.' 
  
  [2] Or breathing in short, he discerns, 'I am breathing in short'; or breathing out short, he discerns, 'I am breathing out short.
  
  Anapanasati Sutta