The problem is that a known bug in the bitcoin protocol has festered for years. If the "core" developers had been doing their job, this problem would have been fixed long ago.
There are a dozen different malleability vectors in the protocol as originally designed; some are quite useful and important intentional features-- others are not. Though the harm from malleability is very moderate-- and because of the intentional features and the potential for ordinary double spends, wallets must have basically sane handling for it--, unwanted third party malleability is a nuisance. In Bitcoin Core's wallet the nuisance can be greatly mitigated by setting spendzeroconfchange=0.
Because of it being a nuisance all of vectors for malleability except for one were blocked as non-standard transactions in Bitcoin Core years ago. The remaining one could not be simply blocked because it requires transactions to confine their signatures to a particular form-- low-S-- and all software was violating before the issue was known. Because of this applying that final constraint would have blocked almost all transactions on the network-- something not justified for a nuisance level attack. Bitcoin Core changed constrain its own transactions to this form in 2013 but it has taken a long time for other software to update themselves. Fortunately, the final remaining type of malleability was ever so slightly trickier to exploit, so people haven't been doing so at scale. In the meantime a proposal was made, as part of BIP62, for a v3 transaction type where parties creating transactions could opt into the protective behavior if they were recent enough to support it. Unfortunately BIP62 is fairly complex and no one outside of a small group of contributors to Bitcoin Core have cared at all about advancing it. So we've been breaking up parts of them and applying them to the consensus incrementally (e.g. BIP66).
Current git master Bitcoin Core
enforces the requirement for all transactions it relays or mines, once this is in a release and widely deployed it will end this irritation; but it will also block most transactions from small portion of the network on software which is out of date or hasn't been updated to produces anti-malleability-friendly low-S signatures (on the order of 5% of all transactions now; due to ongoing efforts to harass parties to fix their wallet software).
I've
called for assistance several times in identifying the origin of a list of lowS violating transactions in order to help speed deployment of this, but it seems that the Bitcoin community is a lot more interested in whining and throwing blame then stepping up and doing a little bit of the non-development work needed to get this deployed.