My guess is that you did
yum install php-ioncube-loader --enablerepo=remi
In place of
yum install php54-php-ioncube-loader --enablerepo=remi
The php version in remi is 5.4, while ours is 5.3. Only php packages starting with php??-php- are scl versions, the first one is to update the main php package which again you do not want to do.
Otherwise if you did the second remi has dependency issues in his repo pointing to the wrong php rpm.
If so you have to open a bug on his site, and or try php55