One of my websites is having canonical issue, does this show any effect on my SEO rankings?

Search engine consider as there are 2 versions of your site. It may be confused to rank. Also it is harmful, as search engine may be consider it as duplicate sites, duplicate content.

Yes, it is good to check canonicalization issue and then proceeding to do SEO since it impacts the search engine bots. 

Having two versions of the same website will result in half of your links going  to one version while the other half going to second version which will directly affect your SERP's.

SE might rank any of the two websites and all your hard work might go waste. A good rule of thumb is that you maintain only one website and optimize it well.

Yes it effects on SEO ranking, sometime inefficient use of canonical can stop that specific web page to gainranking ahead. Especially for the products based website where you are providing different option to users to search over the net and different pages are being generated with same content. 

Hi.
yes, canonical issue may have bad effect on SEO. It will not allow your page to gain the ranking.