I think I messed up chrome settings as I see my extensions showing up near the nav bar. And the only way of hiding them is to right click and "hide in chrome menu" which puts them in the menu as shown on the image. I don't want the extensions to be in chrome menu or show up in the bar, just a default behavior. Any suggestions how to fix this?
You have not messed up your chrome settings. As of version 49, chrome will display all enabled extensions, either in the toolbar or in the menu. The only way to remove an icon is to disable or uninstall the extension.
This was done, presumably, to keep users informed about their installed extensions, becuase lots of users have unitentionally installed extensions that mess up their browser functionality.
Here is Google's help page: Install and manage extensions
Resize the toolbar
Chrome users may resize the area that extensions are allowed to display icons in by hovering with the mouse cursor over the area between the end of the address field and the beginning of the extension icon area, and using the left mouse button to resize the area using drag and drop.
If the area extensions are displayed in is not wide enough to hold all extension icons, those that cannot be displayed there are moved to the top of the Chrome menu instead.
You can verify that easily by clicking on the menu icon to display all leftover extension icons.
Hiding Chrome extensions
It makes no sense to display icons of extensions that require no interaction with the icon. While you may want access to some icons to make use of the extension's functionality whenever the need arises by interacting with it, some extensions may display an icon even though it adds no value whatsoever to the functionality it provides.
Unfortunately, Google implemented the hiding functionality in a way that it is impossible to remove extension icons from the browser UI completely.
While you can right-click on extensions in the Chrome toolbar and select "hide in Chrome menu", doing so will move the icon to the Chrome menu where it will still be displayed.
There is no option available currently to hide the icon of extensions both in the toolbar and the Chrome menu.
The only option available to do that would be to uninstall the extension but that would remove its functionality as well
First what i would do is to go the extensions section and remove/ delete all unwanted stuff.
and if you have google or any other 3rd party tool bar installed (which i do not recommend) try the following:
To change the order of your custom buttons: On your Toolbar, click Settings . Click Customs. To reorder them in the list, drag and drop buttons. You can also click Edit next to a button and click the arrow icons to move it. Click Save.