In the initial stages it is very important that the search engine bots have access to your your contents. Website design should incorporate simple programming and server side includes. Frames and Flash do not work best albeit google bots can now fetch and retrieve readable data from such sites.
Another issue is between http:// and www version of your site. This can be corrected simply by using the webmaster tools and verifying the site. There is an option for which version you prefer set you site to www version since it is more widespread. If you do not do this than you will not get full benefits of promotion if you linking to www version.
Problem with your website's crawling can be detected in the webmaster tools as well. Use the function fetch as Google bot. There are other functions and parameters that can be set according to your preference. There can be several issues at your hosting site one that needs mention is server load which can result in time outs and lack of connectivity. One also needs to renew the domain in time. It is better to renew your domain for more than three years which will make your website more stable on the net.
You have to choose your web hosting carefully. The site retrieval should be quick and it should be protected against malware and virus. If your website is hosted on server with large number of spammy sites then chances of action being taken on whole lot increases.
Using the Google webmaster tools to safe guard your site performance should be a regular activity.