Before discussing about the causes of comprehension, I would first like to define comprehension. It is not merely reading a text and answering the questions much like what is in the English Language exam. Basically, comprehension means the ability to understand something either in speech or written form. It is an action of grasping with the intellect (as Merriam-Webster Dictionary would define) or the processing of information, that is, how fast and how accurate.
To keep it simple, we will just take FIVE main causes of poor comprehension:

1) Limited vocabulary
Limited vocabulary tantamount to the inability to conceive a word’s meaning and restricts a child in expressing himself or herself. Since he cannot grasp meanings and definitions easily, in other words he exhibits poor comprehension, everything is then seen as unattainable. In the end, he will exhibit signs of disinterest and will make hordes of excuses.
2) Working memory having either a deficit or overload
Like a chicken and egg problem, children face difficulty remembering because of the inability to conceptualize an information and hence cannot store it effectively in the brain. Children with reading difficulties face this problem and it has a lot to do with decoding (to be discussed in point 4). As they take much longer time decoding, they will tend to overload their memory bank with the unnecessary and the muddled-up information. Children with ADHD may also face this problem of poor comprehension, too.
3) Disinterest or boredom
With issues like having difficulties concentrating or encountering books that are either too simple or too challenging, might put a child off reading and comprehending. As such, he will not engage himself in this activity and say that the books are a bore. Without parental encouragement and modeling, not making reading a part of their daily routine, will result in him not widening his vocabulary and enlarging his imaginary world.
4) Difficulties in decoding or visually processing information
Decoding is a progressively complex skill we develop as we grow. If a child does not have a good grasp of phonological awareness (the awareness of and ability to work with sounds in spoken language) and phonics, much time is spent decoding the meanings of singular words rather than the story text as a whole unit. He will find it tiring to do this job when others have sailed ahead and so he will give up trying. The problem of remedying his poor comprehension will soon perpetuate and catching up will be an uphill task in the future.
A child with visual processing issue exhibits symptoms like unintentionally skipping words or lines and reversing letters and numbers. As such he cannot build the correct visual scenario and will hence not be able to follow the story or instructions shown.
5) Weak logical and reasoning skills
With under-developed relational thinking and evaluation skills, a child will face great difficulties making connections between words and within sentences/paragraphs. He will not be able to make common sense judgments as the story or information rolls on and will feel lost and hopeless.
Summary
As one can see, the causes of poor comprehension are not isolated but inter-connected. A child that doesn’t read could be because of limited vocabulary or disinterest but the outcome would be him exhibiting poor comprehension. His poor working memory bank will restrict him from sharpening his decoding abilities plus limit his executive functioning skills, as a whole.