This will not cause any problems. I have always setup all MySQL 5.5. DB servers for clients with both plugins. In fact, I answered a question back on Aug 05, 2011 where I posted an update on Aug 08, 2011 on how to install both plugins at the same time

Please see Is MySQL Replication Affected by a High-Latency Interconnect?

Here is the excerpt from that update

EXCERPT

The configuration of MySQL 5.5 Semisynchronous Replication is straightforward

Step 1) Add these four(4) lines to /etc/my.cnf

[mysqld]
plugin-dir=/usr/lib64/mysql/plugin
#rpl_semi_sync_master_enabled
#rpl_semi_sync_master_timeout=5000
#rpl_semi_sync_slave_enabled

Step 2) Restart MySQL

service mysql restart

Step 3) Run these commands in the MySQL client

INSTALL PLUGIN rpl_semi_sync_master SONAME 'semisync_master.so';
INSTALL PLUGIN rpl_semi_sync_slave  SONAME 'semisync_slave.so';

Step 4) Uncomment the three rpm_semi_sync options after the plugin-dir option

[mysqld]
plugin-dir=/usr/lib64/mysql/plugin
rpl_semi_sync_master_enabled
rpl_semi_sync_master_timeout=5000
rpl_semi_sync_slave_enabled

Step 5) Restart MySQL

service mysql restart

All Done !!! Now just setup MySQL Replication as usual.

Using replicate-wild-do-table=% is not the correct way to get complete replication. That would seem sensible, but here's why it isn't:

• The replicate-* options are restrictive by their presence. The *-do-* options seem to be telling the server what to "do," but in fact they are telling the server what to only do.

• The complete absence of any replicate-* configuration variables means "replicate everything."

In the simplest case, when there are no --replicate-* options, the slave executes all statements that it receives from the master. Otherwise, the result depends on the particular options given. -- http://dev.mysql.com/doc/refman/5.5/en/replication-rules.html

That, I think, is the point you are needing. It holds true for all MySQL 5.x.

Once you enable binary logging, set the server-id values on each machine, synchronize the data sets, CHANGE MASTER TO ..., and then START SLAVE, then you should have a working configuration where all DML and DDL will be replicated and your servers will be identical replicas of each other.

If you started out with identical data sets, everything should behave exactly as you would expect it to.

What MySQL replication does best and simplest is replicate entire data sets among servers without any restrictions. Trying to restrict replication to a subset of the data is a process that should carry a warning label that ends with the phrase "...unless you really know what you're doing."

When you use the --replicate-* options, the document cited above also offers this tip:

it is recommended that you avoid mixing “do” and “ignore” options, or wildcard and nonwildcard options

You are using a mix of these, which adds complexity and may explain why your DDL didn't replicate as you expected it to.