Errors and update issue

Have made a few installation of this system that I find very useful and with a nice interface.
But I do have a number of issues with the installation.

By default the error logging is turned of. When I turn this on I get the following error after a clean install.

Notice: Undefined property: view::$dom_id in template_preprocess_views_view() (line 116 of [domain]/profiles/openlucius/modules/contrib/views/theme/theme.inc).
Notice: Undefined offset: 1 in openlucius_core_node_view() (line 3593 of [domain]/profiles/openlucius/modules/openlucius_core/openlucius_core.module).
Notice: Undefined index: identifier in openlucius_menu_link() (line 50 of [domain]/profiles/openlucius/themes/openlucius/template.php).
Notice: Undefined property: view::$dom_id in template_preprocess_views_view() (line 116 of [domain]/profiles/openlucius/modules/contrib/views/theme/theme.inc).
Warning: Invalid argument supplied for foreach() in element_children() (line 6583 of [domain]/includes/common.inc).
Warning: Cannot use a scalar value as an array in drupal_render() (line 6040 of [domain]/includes/common.inc).
Warning: Cannot use a scalar value as an array in drupal_render() (line 6095 of [domain]/includes/common.inc).
Warning: Invalid argument supplied for foreach() in element_children() (line 6583 of [domain]/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 6040 of [domain]/includes/common.inc).
Warning: Cannot assign an empty string to a string offset in drupal_render() (line 6040 of [domain]/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 6050 of [domain]/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 6088 of [domain]/includes/common.inc).
Warning: Illegal string offset '#printed' in drupal_render() (line 6095 of [domain]/includes/common.inc).

--- there are more lines but some are being repeated. I have altered the list of error (removed the full path).

When making a reply to a task I get those errors again and some extra:
×Error message
Notice: Undefined index: group in openlucius_core_extract_values() (line 412 of [domain]/profiles/openlucius/modules/openlucius_core/includes/modal.inc).
Notice: Undefined index: identifier in openlucius_menu_link() (line 50 of [domain]/profiles/openlucius/themes/openlucius/template.php).
Notice: Undefined property: view::$dom_id in template_preprocess_views_view() (line 116 of [domain]/profiles/openlucius/modules/contrib/views/theme/theme.inc).
Notice: Undefined index: node in openlucius_preprocess_page() (line 1062 of [domain]/profiles/openlucius/themes/openlucius/template.php).
Notice: Trying to get property of non-object in openlucius_preprocess_page() (line 1062 of [domain]/profiles/openlucius/themes/openlucius/template.php).

Going to the configuration page new errors shows.

I also have a number of modules that needs to be updated - included Drupal Core.

If I run an update of all, the list of errors expand with many more errors and certain things do not work after an update:
- an error message (popup windows, Ajax) when making replying to a task (because the "Comment Alter" should not have been updated)
- TimeTracker stopped working - I think I got it to work before the update, but not absolutely sure about that.

I would like to keep all modules updated but after spending hours finding that a module update caused the error with replying.
I would like to know what modules are not safe to update?
Will the install file be updated with correct modules and Drupal Core soon?

But for now, how do I get this errors solved - it is not a solution just to turn the error messages off - errors needs to be solved in an active environment.

Can any one help with more information?