WordPress dbDelta returns a SQL error when updating a table. It returns “Multiple primary key defined“.
I was stuck for two days on this problem. WordPress shown me following error message on plugin activation

I searched for the main cause. I edited WordPress core file to save the output that was being generated on plugin activation. I found WP returns following MySQL error on behind.

But I could not find the sql syntax error in my query. My query is bellow.

$my_stat_sql = "CREATE TABLE IF NOT EXISTS `$my_stat_table` (
	  `id` bigint(20) NOT NULL auto_increment,
	  `cid` bigint(20) NOT NULL,
	  `v_time` datetime NOT NULL,
	  `ip` varchar(20) NOT NULL,
	  PRIMARY KEY  (`id`)
	) ENGINE=MyISAM  DEFAULT CHARSET=utf8;
	";

	dbDelta($my_stat_sql);

Are you see any error on above codes? probably not.

Finally I got the solution.

Actually WP dbDelta can not handle when you use PRIMARY KEY (`id`) with back-tick (`) any single or double quote , or space between columns names like PRIMARY KEY (“id, pid”).
I removed the back-ticks (`) from my query when assigning the primary keys. PRIMARY KEY (id). My issue has been solved. My new codes is bellow

$my_stat_sql = "CREATE TABLE IF NOT EXISTS `$my_stat_table` (
	  `id` bigint(20) NOT NULL auto_increment,
	  `cid` bigint(20) NOT NULL,
	  `v_time` datetime NOT NULL,
	  `ip` varchar(20) NOT NULL,
	  PRIMARY KEY  (id)
	) ENGINE=MyISAM  DEFAULT CHARSET=utf8;
	";

	dbDelta($my_stat_sql);

More problem I found. My plugin returns error on installation yet. Got error : [Multiple primary key defined] ALTER TABLE my_stat_table ADD PRIMARY KEY (id)
After a long experiment I decided to use UNIQUE KEY.
Now I am using UNIQUE KEY id (id) instead of PRIMARY KEY (id)
because dbDelta were returning error “[Multiple primary key defined]”
Difference between PRIMARY KEY and UNIQUE KEY
Primary keys and unique keys are similar. A primary key is a column, or a combination of columns, that can uniquely identify a row. It is a special case of unique key. A table can have at most one primary key, but more than one unique key. When you specify a unique key on a column, no two distinct rows in a table can have the same value.
Read : Discussion 1 , Discussion 2

I saw my plugin table is not being updated with new column on plugin activation.
I stopped using “IF NOT EXISTS” with create table because, if I use this, dbdelta don’t update my table.
I removed all back tick(`) from all column name and table name to be more safe.

SO NOW MY FINAL ERROR FREE CODE IS :

$my_stat_sql = "CREATE TABLE IF NOT EXISTS $my_stat_table (
	  id bigint(20) NOT NULL auto_increment,
	  cid bigint(20) NOT NULL,
	  v_time datetime NOT NULL,
	  ip varchar(20) NOT NULL,
	  UNIQUE KEY id (id)
	) ENGINE=MyISAM  DEFAULT CHARSET=utf8;
	";

	dbDelta($my_stat_sql);

Read more detail about WordPress dbDelta Function and core documentation about dbDelta and creating tables with plugin